From 673364cd3a7848067dc3ecb69c7f8a4f3a28f6d5 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sun, 21 Oct 2018 19:49:10 +0200 Subject: [PATCH 01/58] gnu: Add emacs-slime-repl-ansi-color. * gnu/packages/emacs.scm (emacs-slime-repl-ansi-color): New variable. --- gnu/packages/emacs.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 1069b9e3c3..47e984e101 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -12386,3 +12386,23 @@ (define-public emacs-column-marker distances. Multi-column characters, such as @kbd{TAB} are treated correctly.") (license license:gpl2+))) + +(define-public emacs-slime-repl-ansi-color + (let ((commit "ad03263f5d4de473bc173b64a6fc3dc1106393d7")) + (package + (name "emacs-slime-repl-ansi-color") + (version (git-version "0.0.0" "1" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/deadtrickster/slime-repl-ansi-color") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0bpg7gxz310x7bnlg324c507sxc5gxwwz6h64h6kdq141r73vbi4")))) + (build-system emacs-build-system) + (home-page "https://github.com/deadtrickster/slime-repl-ansi-color") + (synopsis "Color ANSI codes in the REPL of SLIME") + (description "Color ANSI codes in the REPL of SLIME") + (license license:gpl2+)))) From 9ab6c680ba7e42d3a7cf13c74a7bbcb53c5c390e Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Sun, 21 Oct 2018 14:56:44 -0400 Subject: [PATCH 02/58] gnu: linux-libre@4.4: Update to 4.4.162. * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.162. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 2aeddc2a34..5cbf87b68c 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -452,8 +452,8 @@ (define-public linux-libre-4.9 #:configuration-file kernel-config)) (define-public linux-libre-4.4 - (make-linux-libre "4.4.161" - "1q6bsndpjgw72mybhl5l8vrxs4mimg6821bjgi1pjkxbc7nd921b" + (make-linux-libre "4.4.162" + "1anb2k9i03369lvbwlw24vimxvk8zpcql4ryz0ydvf3pxv8lirm2" %intel-compatible-systems #:configuration-file kernel-config)) From c4a7a512922467313f5cc18fc61029c44ac5360e Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Sun, 21 Oct 2018 14:57:24 -0400 Subject: [PATCH 03/58] gnu: linux-libre@4.9: Update to 4.9.135. * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.135. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 5cbf87b68c..09f64d5e04 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -446,8 +446,8 @@ (define-public linux-libre-4.14 #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.134" - "0f5qif27k0mhc57d98arbfkq7zlvg0ra2gz6g5fasblyjz3j7w7h" + (make-linux-libre "4.9.135" + "07v5s6hl08ls2z9xdkbqq1s210mqayfchqbckhp8hlaw089ap71f" %intel-compatible-systems #:configuration-file kernel-config)) From 668834cae0f6b761d88533c91475d9184a8ab4ad Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Sun, 21 Oct 2018 14:58:03 -0400 Subject: [PATCH 04/58] gnu: linux-libre@4.14: Update to 4.14.78. * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.78. (%linux-libre-4.14-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 09f64d5e04..61560b7a1b 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -436,8 +436,8 @@ (define-public linux-libre #:patches %linux-libre-4.18-patches #:configuration-file kernel-config)) -(define %linux-libre-4.14-version "4.14.77") -(define %linux-libre-4.14-hash "18y81rga2lhsk7bjckglxz52pvnzf103ar0z2zj611g37wyf83r5") +(define %linux-libre-4.14-version "4.14.78") +(define %linux-libre-4.14-hash "07dhhw6zdnqn2dznpmkniz58hfkdx89yx7csm9vbx45blnyhjw5z") (define-public linux-libre-4.14 (make-linux-libre %linux-libre-4.14-version From f7618bf18e00f6ece8e886f2fc6328314d1ed544 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Sun, 21 Oct 2018 14:59:30 -0400 Subject: [PATCH 05/58] gnu: linux-libre: Update to 4.18.16. * gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.16. (%linux-libre-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 61560b7a1b..bc53a88bfc 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -405,8 +405,8 @@ (define %linux-compatible-systems '("x86_64-linux" "i686-linux" "armhf-linux" "a ;; supports qemu "virt" machine and possibly a large number of ARM boards. ;; See : https://wiki.debian.org/DebianKernel/ARMMP. -(define %linux-libre-version "4.18.15") -(define %linux-libre-hash "0v6xs85qn1iy2dj3m6s3cfnhbwb1mjy21d9lagjni8dg3jic26hf") +(define %linux-libre-version "4.18.16") +(define %linux-libre-hash "15apfgswp2lrwjpi3vwnanlkdw3q6rkvwrbgrb71rjsy9gazlz62") (define %linux-libre-4.18-patches (list %boot-logo-patch From 9a6808e0c00d6acb00b7be4aa573f252fa7d9635 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 11:54:44 +0200 Subject: [PATCH 06/58] gnu: tophat: Update to 2.1.1. * gnu/packages/bioinformatics.scm (tophat): Update to 2.1.1. * gnu/packages/patches/tophat-build-with-later-seqan.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. --- gnu/local.mk | 1 - gnu/packages/bioinformatics.scm | 7 +++--- .../tophat-build-with-later-seqan.patch | 24 ------------------- 3 files changed, 3 insertions(+), 29 deletions(-) delete mode 100644 gnu/packages/patches/tophat-build-with-later-seqan.patch diff --git a/gnu/local.mk b/gnu/local.mk index 1c48fd3d6e..c167e6753c 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1177,7 +1177,6 @@ dist_patch_DATA = \ %D%/packages/patches/tk-find-library.patch \ %D%/packages/patches/ttf2eot-cstddef.patch \ %D%/packages/patches/ttfautohint-source-date-epoch.patch \ - %D%/packages/patches/tophat-build-with-later-seqan.patch \ %D%/packages/patches/totem-meson-easy-codec.patch \ %D%/packages/patches/tuxpaint-stamps-path.patch \ %D%/packages/patches/twinkle-include-qregexpvalidator.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1e04081ceb..0dc81c8f61 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1332,7 +1332,7 @@ (define-public bowtie (define-public tophat (package (name "tophat") - (version "2.1.0") + (version "2.1.1") (source (origin (method url-fetch) (uri (string-append @@ -1340,13 +1340,12 @@ (define-public tophat version ".tar.gz")) (sha256 (base32 - "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7")) - (patches (search-patches "tophat-build-with-later-seqan.patch")) + "19add02kv2xhd6ihd779dr7x35ggym3jqr0m5c4315i1yfb0p11p")) (modules '((guix build utils))) (snippet '(begin ;; Remove bundled SeqAn and samtools - (delete-file-recursively "src/SeqAn-1.3") + (delete-file-recursively "src/SeqAn-1.4.2") (delete-file-recursively "src/samtools-0.1.18") #t)))) (build-system gnu-build-system) diff --git a/gnu/packages/patches/tophat-build-with-later-seqan.patch b/gnu/packages/patches/tophat-build-with-later-seqan.patch deleted file mode 100644 index fc742e2a7d..0000000000 --- a/gnu/packages/patches/tophat-build-with-later-seqan.patch +++ /dev/null @@ -1,24 +0,0 @@ -This patch resolves a build failure when building TopHat 2.1.0 with SeqAn 1.4. -This is the relevant part of a patch originally posted here: -https://lists.fu-berlin.de/pipermail/seqan-dev/2014-July/msg00001.html - ---- a/src/segment_juncs.cpp -+++ b/src/segment_juncs.cpp -@@ -2050,10 +2050,13 @@ void juncs_from_ref_segs(RefSequenceTabl - typedef map MotifMap; - - MotifMap ims; -- -- seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc); -- seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc); -- -+ -+ typedef seqan::ModifiedString< -+ seqan::ModifiedString > >, -+ seqan::ModReverse> ConstDnaStringReverseComplement; -+ ConstDnaStringReverseComplement rev_donor_dinuc(donor_dinuc); -+ ConstDnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc); -+ - if (talkative) - fprintf(stderr, "Collecting potential splice sites in islands\n"); - From 1d18ee6dfd99d9945a0e8eae7557250a1bdc6306 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 12:00:41 +0200 Subject: [PATCH 07/58] gnu: bwa-pssm: Fetch from git. * gnu/packages/bioinformatics.scm (bwa-pssm)[source]: Fetch from git. --- gnu/packages/bioinformatics.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0dc81c8f61..593b5b6202 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1449,13 +1449,14 @@ (define-public bwa-pssm (name "bwa-pssm") (version "0.5.11") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/" - "archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/pkerpedjiev/bwa-pssm.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg")))) + "076c4q0cdqz8jgylb067y9zmvxglppnzi3qiscn0xiypgc6lgb5r")))) (build-system gnu-build-system) (inputs `(("gdsl" ,gdsl) From 2ba2d62c69409255e0c00c480c424c668cba845f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 12:33:01 +0200 Subject: [PATCH 08/58] gnu: python2-bx-python: Update to 0.8.2. * gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.8.2. [source]: Remove obsolete snippet. [inputs]: Move python2-numpy from here... [propagated-inputs]: ...to here; add python2-six. [native-inputs]: Add python2-lzo and python2-cython. [home-page]: Update to new home at Github. --- gnu/packages/bioinformatics.scm | 24 ++++++++++-------------- 1 file changed, 10 insertions(+), 14 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 593b5b6202..dee8a975b9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1477,31 +1477,27 @@ (define-public bwa-pssm (define-public python2-bx-python (package (name "python2-bx-python") - (version "0.7.3") + (version "0.8.2") (source (origin (method url-fetch) (uri (pypi-uri "bx-python" version)) (sha256 (base32 - "15z2w3bvnc0n4qmb9bd6d8ylc2h2nj883x2w9iixf4x3vki9b22i")) - (modules '((guix build utils))) - (snippet - '(begin - (substitute* "setup.py" - ;; remove dependency on outdated "distribute" module - (("^from distribute_setup import use_setuptools") "") - (("^use_setuptools\\(\\)") "")) - #t)))) + "11kksg2rbzihpmcid823xvg42xi88m7sz58rzk29abybkxy0rszs")))) (build-system python-build-system) (arguments `(#:tests? #f ;tests fail because test data are not included #:python ,python-2)) - (inputs + (propagated-inputs `(("python-numpy" ,python2-numpy) - ("zlib" ,zlib))) + ("python-six" ,python2-six))) + (inputs + `(("zlib" ,zlib))) (native-inputs - `(("python-nose" ,python2-nose))) - (home-page "http://bitbucket.org/james_taylor/bx-python/") + `(("python-lzo" ,python2-lzo) + ("python-nose" ,python2-nose) + ("python-cython" ,python2-cython))) + (home-page "https://github.com/bxlab/bx-python") (synopsis "Tools for manipulating biological data") (description "bx-python provides tools for manipulating biological data, particularly From f5cec0068a7e6f9ca1b7542d1839b832ee057648 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 12:36:53 +0200 Subject: [PATCH 09/58] gnu: Add python-bx-python. * gnu/packages/bioinformatics.scm (python-bx-python): New variable. (python2-bx-python): Define in terms of python-bx-python. --- gnu/packages/bioinformatics.scm | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dee8a975b9..7cd9172446 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1474,9 +1474,9 @@ (define-public bwa-pssm well as many of the command line options.") (license license:gpl3+))) -(define-public python2-bx-python +(define-public python-bx-python (package - (name "python2-bx-python") + (name "python-bx-python") (version "0.8.2") (source (origin (method url-fetch) @@ -1485,18 +1485,17 @@ (define-public python2-bx-python (base32 "11kksg2rbzihpmcid823xvg42xi88m7sz58rzk29abybkxy0rszs")))) (build-system python-build-system) - (arguments - `(#:tests? #f ;tests fail because test data are not included - #:python ,python-2)) + ;; Tests fail because test data are not included + (arguments '(#:tests? #f)) (propagated-inputs - `(("python-numpy" ,python2-numpy) - ("python-six" ,python2-six))) + `(("python-numpy" ,python-numpy) + ("python-six" ,python-six))) (inputs `(("zlib" ,zlib))) (native-inputs - `(("python-lzo" ,python2-lzo) - ("python-nose" ,python2-nose) - ("python-cython" ,python2-cython))) + `(("python-lzo" ,python-lzo) + ("python-nose" ,python-nose) + ("python-cython" ,python-cython))) (home-page "https://github.com/bxlab/bx-python") (synopsis "Tools for manipulating biological data") (description @@ -1504,6 +1503,9 @@ (define-public python2-bx-python multiple sequence alignments.") (license license:expat))) +(define-public python2-bx-python + (package-with-python2 python-bx-python)) + (define-public python-pysam (package (name "python-pysam") From 8640f9ec91f7a9e81457a3651a06465fd8dd03a3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 12:42:14 +0200 Subject: [PATCH 10/58] gnu: python-twobitreader: Update to 3.1.6. * gnu/packages/bioinformatics.scm (python-twobitreader): Update to 3.1.6. [source]: Fetch from git. --- gnu/packages/bioinformatics.scm | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7cd9172446..795b0f208e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1595,19 +1595,19 @@ (define-public python2-pysam (define-public python-twobitreader (package (name "python-twobitreader") - (version "3.1.4") + (version "3.1.6") (source (origin - (method url-fetch) - (uri (pypi-uri "twobitreader" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/benjschiller/twobitreader") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1q8wnj2kga9nz1lwc4w7qv52smfm536hp6mc8w6s53lhyj0mpi22")))) + "1qbxvv1h58cismbk1anpjrkpghsaiy64a11ir3lhy6qch6xf8n62")))) (build-system python-build-system) - (arguments - '(;; Tests are not distributed in the PyPi release. - ;; TODO Try building from the Git repo or asking the upstream maintainer - ;; to distribute the tests on PyPi. - #:tests? #f)) + ;; Tests are not included + (arguments '(#:tests? #f)) (native-inputs `(("python-sphinx" ,python-sphinx))) (home-page "https://github.com/benjschiller/twobitreader") From 7321920cd3c9c1d7532024dfcdb958cce54b6368 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 12:51:31 +0200 Subject: [PATCH 11/58] gnu: crossmap: Update to 0.2.9. * gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.9. * gnu/packages/patches/crossmap-allow-system-pysam.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. --- gnu/local.mk | 1 - gnu/packages/bioinformatics.scm | 25 +--- .../patches/crossmap-allow-system-pysam.patch | 121 ------------------ 3 files changed, 6 insertions(+), 141 deletions(-) delete mode 100644 gnu/packages/patches/crossmap-allow-system-pysam.patch diff --git a/gnu/local.mk b/gnu/local.mk index c167e6753c..c76908f92f 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -634,7 +634,6 @@ dist_patch_DATA = \ %D%/packages/patches/cracklib-fix-buffer-overflow.patch \ %D%/packages/patches/crawl-upgrade-saves.patch \ %D%/packages/patches/crda-optional-gcrypt.patch \ - %D%/packages/patches/crossmap-allow-system-pysam.patch \ %D%/packages/patches/clucene-contribs-lib.patch \ %D%/packages/patches/cube-nocheck.patch \ %D%/packages/patches/cursynth-wave-rand.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 795b0f208e..6469e9e1a1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1894,31 +1894,18 @@ (define-public clustal-omega (define-public crossmap (package (name "crossmap") - (version "0.2.1") + (version "0.2.9") (source (origin (method url-fetch) - (uri (string-append "mirror://sourceforge/crossmap/CrossMap-" - version ".tar.gz")) + (uri (pypi-uri "CrossMap" version)) (sha256 (base32 - "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f")) - ;; This patch has been sent upstream already and is available - ;; for download from Sourceforge, but it has not been merged. - (patches (search-patches "crossmap-allow-system-pysam.patch")) - (modules '((guix build utils))) - (snippet '(begin - ;; remove bundled copy of pysam - (delete-file-recursively "lib/pysam") - #t)))) + "1byhclrqnqpvc1rqkfh4jwj6yhn0x9y7jk47i0qcjlhk0pjkw92p")))) (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'set-env - (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1") #t))))) + (arguments `(#:python ,python-2)) (inputs - `(("python-numpy" ,python2-numpy) + `(("python-bx-python" ,python2-bx-python) + ("python-numpy" ,python2-numpy) ("python-pysam" ,python2-pysam) ("zlib" ,zlib))) (native-inputs diff --git a/gnu/packages/patches/crossmap-allow-system-pysam.patch b/gnu/packages/patches/crossmap-allow-system-pysam.patch deleted file mode 100644 index 611c4ff74d..0000000000 --- a/gnu/packages/patches/crossmap-allow-system-pysam.patch +++ /dev/null @@ -1,121 +0,0 @@ -This patch modifies the build process such that the bundled copy of pysam does -not need to be built if CROSSMAP_USE_SYSTEM_PYSAM is set and the pysam module -can be imported. - -Upstream has agreed to apply the patch in the next maintenance release of -crossmap. The patch has already been uploaded to -http://sourceforge.net/projects/crossmap/files/patch/. - -diff --git a/setup.py b/setup.py ---- a/setup.py 2015-02-26 15:28:49.771189185 +0100 -+++ b/setup.py 2015-02-26 15:55:03.440327752 +0100 -@@ -19,6 +19,15 @@ - except: - have_numpy = False - -+try: -+ import pysam -+ if os.environ['CROSSMAP_USE_SYSTEM_PYSAM']: -+ have_pysam = True -+ else: -+ have_pysam = False -+except ImportError: -+ have_pysam = False -+ - if platform.system()=='Windows': - print >> sys.stderr, "Sorry, Windows platform is not supported!" - sys.exit() -@@ -165,49 +174,50 @@ - - - #================= pysam samtools ==================== -- extensions.append(Extension( -- "pysam.csamtools", -- csamtools_sources + [ "lib/pysam/%s" % x for x in ("pysam_util.c", )] +\ -- glob.glob( os.path.join( "lib/samtools", "*.pysam.c" )) +\ -- os_c_files + \ -- glob.glob( os.path.join( "lib/samtools", "*", "*.pysam.c" ) ), -- library_dirs=[], -- include_dirs=[ "lib/samtools", "lib/pysam" ] + include_os, -- libraries=[ "z", ], -- language="c", -- define_macros = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')], -- )) -- -- extensions.append(Extension( -- "pysam.ctabix", -- tabix_sources + [ "lib/pysam/%s" % x for x in ( "tabix_util.c", )] +\ -- os_c_files + \ -- glob.glob( os.path.join( "lib/tabix", "*.pysam.c" ) ), -- library_dirs=[], -- include_dirs=[ "lib/tabix", "lib/pysam" ] + include_os, -- libraries=[ "z", ], -- language="c", -- define_macros = [('_FILE_OFFSET_BITS','64'), -- ('_USE_KNETFILE','')], -- )) -- -- extensions.append(Extension( -- "pysam.TabProxies", -- tabproxies_sources + os_c_files, -- library_dirs=[], -- include_dirs= include_os, -- libraries=[ "z", ], -- language="c", -- )) -- -- extensions.append(Extension( -- "pysam.cvcf", -- cvcf_sources + os_c_files, -- library_dirs=[], -- include_dirs= ["lib/tabix",] + include_os, -- libraries=[ "z", ], -- language="c", -- )) -+ if not have_pysam: -+ extensions.append(Extension( -+ "pysam.csamtools", -+ csamtools_sources + [ "lib/pysam/%s" % x for x in ("pysam_util.c", )] +\ -+ glob.glob( os.path.join( "lib/samtools", "*.pysam.c" )) +\ -+ os_c_files + \ -+ glob.glob( os.path.join( "lib/samtools", "*", "*.pysam.c" ) ), -+ library_dirs=[], -+ include_dirs=[ "lib/samtools", "lib/pysam" ] + include_os, -+ libraries=[ "z", ], -+ language="c", -+ define_macros = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')], -+ )) -+ -+ extensions.append(Extension( -+ "pysam.ctabix", -+ tabix_sources + [ "lib/pysam/%s" % x for x in ( "tabix_util.c", )] +\ -+ os_c_files + \ -+ glob.glob( os.path.join( "lib/tabix", "*.pysam.c" ) ), -+ library_dirs=[], -+ include_dirs=[ "lib/tabix", "lib/pysam" ] + include_os, -+ libraries=[ "z", ], -+ language="c", -+ define_macros = [('_FILE_OFFSET_BITS','64'), -+ ('_USE_KNETFILE','')], -+ )) -+ -+ extensions.append(Extension( -+ "pysam.TabProxies", -+ tabproxies_sources + os_c_files, -+ library_dirs=[], -+ include_dirs= include_os, -+ libraries=[ "z", ], -+ language="c", -+ )) -+ -+ extensions.append(Extension( -+ "pysam.cvcf", -+ cvcf_sources + os_c_files, -+ library_dirs=[], -+ include_dirs= ["lib/tabix",] + include_os, -+ libraries=[ "z", ], -+ language="c", -+ )) - - - return extensions From a5b0038cbdfd8ad81472279089aaebc4270c683a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 12:57:43 +0200 Subject: [PATCH 12/58] gnu: Add python-dnaio. * gnu/packages/bioinformatics.scm (python-dnaio): New variable. --- gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6469e9e1a1..58b29e2a30 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1919,6 +1919,29 @@ (define-public crossmap file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") (license license:gpl2+))) +(define-public python-dnaio + (package + (name "python-dnaio") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "dnaio" version)) + (sha256 + (base32 + "0f16m7hdlm0fz1n7y5asy0v9ghyrq17ni1p9iybq22ddzyd49r27")))) + (build-system python-build-system) + (native-inputs + `(("python-cython" ,python-cython) + ("python-pytest" ,python-pytest) + ("python-xopen" ,python-xopen))) + (home-page "https://github.com/marcelm/dnaio/") + (synopsis "Read FASTA and FASTQ files efficiently") + (description + "dnaio is a Python library for fast parsing of FASTQ and also FASTA +files. The code was previously part of the cutadapt tool.") + (license license:expat))) + (define-public cutadapt (package (name "cutadapt") From 6b7260bad124d3d63ce5ae305d7b74da28e9a947 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 12:57:53 +0200 Subject: [PATCH 13/58] gnu: cutadapt: Update to 1.18. * gnu/packages/bioinformatics.scm (cutadapt): Update to 1.18. [inputs]: Add python-dnaio. --- gnu/packages/bioinformatics.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 58b29e2a30..995cbc76eb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1945,19 +1945,20 @@ (define-public python-dnaio (define-public cutadapt (package (name "cutadapt") - (version "1.16") + (version "1.18") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/marcelm/cutadapt.git") (commit (string-append "v" version)))) - (file-name (string-append name "-" version "-checkout")) + (file-name (git-file-name name version)) (sha256 (base32 - "09pr02067jiks19nc0aby4xp70hhgvb554i2y1c04rv1m401w7q8")))) + "08bbfwyc0kvcd95jf2s95xiv9s3cbsxm39ydl0qck3fw3cviwxpg")))) (build-system python-build-system) (inputs - `(("python-xopen" ,python-xopen))) + `(("python-dnaio" ,python-dnaio) + ("python-xopen" ,python-xopen))) (native-inputs `(("python-cython" ,python-cython) ("python-pytest" ,python-pytest))) From 6b31040ae6865436c1a21378a8b9a09e25ec4adc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 13:42:22 +0200 Subject: [PATCH 14/58] gnu: python-py2bit: Update to 0.3.0. * gnu/packages/bioinformatics.scm (python-py2bit): Update to 0.3.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 995cbc76eb..feb4928a93 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2091,14 +2091,14 @@ (define-public python2-dendropy (define-public python-py2bit (package (name "python-py2bit") - (version "0.2.1") + (version "0.3.0") (source (origin (method url-fetch) (uri (pypi-uri "py2bit" version)) (sha256 (base32 - "1cdf4qlmgwsh1f4k0wdv2sr8x9qn4366p0k3614vbd0fpqiarxrl")))) + "1vw2nvw1yrl7ikkqsqs1pg239yr5nspvd969r1x9arms1k25a1a5")))) (build-system python-build-system) (home-page "https://github.com/dpryan79/py2bit") (synopsis "Access 2bit files using lib2bit") From 42643fc24dd1f418f5f2e0991181d526c0419c1a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 13:43:07 +0200 Subject: [PATCH 15/58] gnu: python-dendropy: Fetch from git. * gnu/packages/bioinformatics.scm (python-dendropy)[source]: Fetch from git. --- gnu/packages/bioinformatics.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index feb4928a93..60e8f6e55a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2053,15 +2053,15 @@ (define-public python-dendropy (version "4.4.0") (source (origin - (method url-fetch) + (method git-fetch) ;; Source from GitHub so that tests are included. - (uri - (string-append "https://github.com/jeetsukumaran/DendroPy/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (uri (git-reference + (url "https://github.com/jeetsukumaran/DendroPy.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0v2fccny5xjaah546bsch1mw4kh61qq5frz2ibllxs9mp6ih9bsn")))) + "097hfyv2kaf4x92i4rjx0paw2cncxap48qivv8zxng4z7nhid0x9")))) (build-system python-build-system) (home-page "http://packages.python.org/DendroPy/") (synopsis "Library for phylogenetics and phylogenetic computing") From e6b65bd219a909514b32a46536a94e288da006fd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 13:43:33 +0200 Subject: [PATCH 16/58] gnu: eolie: Update to 0.9.45. * gnu/packages/gnome.scm (eolie): Update to 0.9.45. --- gnu/packages/gnome.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 7d2742f08d..4b94b2f271 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -4092,15 +4092,15 @@ (define-public simple-scan (define-public eolie (package (name "eolie") - (version "0.9.38") + (version "0.9.45") (source (origin (method url-fetch) (uri (string-append "https://gitlab.gnome.org/World/eolie/" - "uploads/9814c06a1bc83ea09c3da8719a9ed11b/" + "uploads/020f3f686e2b938731752a1d9f5bfa7e/" "eolie-" version ".tar.xz")) (sha256 (base32 - "10vrh91rapgfmqwc6jkcybpmlvn4q0y8bnklw3rddzigf9kvqsff")))) + "0371p7g13r0b7zjc48fdcil43ddwpmyvkd2a4vv6ifsqmny6kl42")))) (build-system meson-build-system) (arguments `(#:glib-or-gtk? #t From 4d494a4fa3ebb2d1deacede405d0b0d8e5dbc32b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 13:52:27 +0200 Subject: [PATCH 17/58] gnu: deeptools: Update to 3.1.3. * gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 60e8f6e55a..bc21848367 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2110,7 +2110,7 @@ (define-public python-py2bit (define-public deeptools (package (name "deeptools") - (version "3.1.2") + (version "3.1.3") (source (origin (method git-fetch) (uri (git-reference @@ -2119,7 +2119,7 @@ (define-public deeptools (file-name (git-file-name name version)) (sha256 (base32 - "06fdpp6cg3xiwryxjhixvfysl4z0ps1crjgia587qa9ikqpsa7fd")))) + "1vggnf52g6q2vifdl4cyi7s2fnfqq0ky2zrkj5zv2qfzsc3p3siw")))) (build-system python-build-system) (arguments `(#:phases From 7a1e62ca67849f9ca19ded4d26c542021db71e38 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 14:00:07 +0200 Subject: [PATCH 18/58] gnu: delly: Update to 0.7.9. * gnu/packages/bioinformatics.scm (delly): Update to 0.7.9. [source]: Fetch from git. [arguments]: Add phase install-templates; use default install phase. [native-inputs]: Remove python-2. [home-page]: Use new home page. * gnu/packages/patches/delly-use-system-libraries.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. --- gnu/local.mk | 1 - gnu/packages/bioinformatics.scm | 40 ++++++------- .../patches/delly-use-system-libraries.patch | 56 ------------------- 3 files changed, 20 insertions(+), 77 deletions(-) delete mode 100644 gnu/packages/patches/delly-use-system-libraries.patch diff --git a/gnu/local.mk b/gnu/local.mk index c76908f92f..d155b4c613 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -642,7 +642,6 @@ dist_patch_DATA = \ %D%/packages/patches/datamash-arm-tests.patch \ %D%/packages/patches/dbus-helper-search-path.patch \ %D%/packages/patches/deja-dup-use-ref-keyword-for-iter.patch \ - %D%/packages/patches/delly-use-system-libraries.patch \ %D%/packages/patches/dfu-programmer-fix-libusb.patch \ %D%/packages/patches/diffutils-gets-undeclared.patch \ %D%/packages/patches/diffutils-getopt.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bc21848367..78debbc873 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2155,42 +2155,42 @@ (define-public deeptools (define-public delly (package (name "delly") - (version "0.7.7") + (version "0.7.9") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/tobiasrausch/delly/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/dellytools/delly.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "0dkwy3pyxmi6dhh1lpsr3698ri5sslw9qz67hfys0bz8dgrqwabj")) - (patches (search-patches "delly-use-system-libraries.patch")))) + (base32 "034jqsxswy9gqdh2zkgc1js99qkv75ks4xvzgmh0284sraagv61z")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "src/htslib") + #t)))) (build-system gnu-build-system) (arguments `(#:tests? #f ; There are no tests to run. - #:make-flags '("PARALLEL=1") ; Allow parallel execution at run-time. + #:make-flags + (list "PARALLEL=1" ; Allow parallel execution at run-time. + (string-append "prefix=" (assoc-ref %outputs "out"))) #:phases (modify-phases %standard-phases (delete 'configure) ; There is no configure phase. - (replace 'install - (lambda _ - (let ((bin (string-append (assoc-ref %outputs "out") "/bin")) - (templates (string-append (assoc-ref %outputs "out") + (add-after 'install 'install-templates + (lambda* (#:key outputs #:allow-other-keys) + (let ((templates (string-append (assoc-ref outputs "out") "/share/delly/templates"))) - (mkdir-p bin) (mkdir-p templates) (copy-recursively "excludeTemplates" templates) - (install-file "src/cov" bin) - (install-file "src/delly" bin) - (install-file "src/dpe" bin))))))) - (native-inputs - `(("python" ,python-2))) + #t)))))) (inputs `(("boost" ,boost) ("htslib" ,htslib) ("zlib" ,zlib) ("bzip2" ,bzip2))) - (home-page "https://github.com/tobiasrausch/delly") + (home-page "https://github.com/dellytools/delly") (synopsis "Integrated structural variant prediction method") (description "Delly is an integrated structural variant prediction method that can discover and genotype deletions, tandem duplications, inversions and diff --git a/gnu/packages/patches/delly-use-system-libraries.patch b/gnu/packages/patches/delly-use-system-libraries.patch deleted file mode 100644 index 3315c2a176..0000000000 --- a/gnu/packages/patches/delly-use-system-libraries.patch +++ /dev/null @@ -1,56 +0,0 @@ ---- a/Makefile 2017-04-09 12:48:15.000000000 +0200 -+++ b/Makefile 2017-06-21 14:26:02.749282787 +0200 -@@ -9,8 +9,8 @@ - - # Flags - CXX=g++ --CXXFLAGS += -isystem ${SEQTK_ROOT} -isystem ${BOOST_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing --LDFLAGS += -L${SEQTK_ROOT} -L${BOOST_ROOT}/stage/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -+CXXFLAGS += -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing -+LDFLAGS += -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time - - # Additional flags for release/debug - ifeq (${PARALLEL}, 1) -@@ -23,7 +23,7 @@ - ifeq (${STATIC}, 1) - LDFLAGS += -static -static-libgcc -pthread -lhts -lz - else -- LDFLAGS += -lhts -lz -Wl,-rpath,${SEQTK_ROOT},-rpath,${BOOST_ROOT}/stage/lib -+ LDFLAGS += -lhts -lz - endif - ifeq (${DEBUG}, 1) - CXXFLAGS += -g -O0 -fno-inline -DDEBUG -@@ -41,29 +41,17 @@ - DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp) - - # Targets --TARGETS = .htslib .bcftools .boost src/delly src/cov src/dpe -+TARGETS = src/delly src/cov src/dpe - - all: $(TARGETS) - --.htslib: $(HTSLIBSOURCES) -- cd src/htslib && make && make lib-static && cd ../../ && touch .htslib -- --.bcftools: $(HTSLIBSOURCES) -- cd src/bcftools && make && cd ../../ && touch .bcftools -- --.boost: $(BOOSTSOURCES) -- cd src/modular-boost && ./bootstrap.sh --prefix=${PWD}/src/modular-boost --without-icu --with-libraries=iostreams,filesystem,system,program_options,date_time && ./b2 && ./b2 headers && cd ../../ && touch .boost -- --src/delly: .htslib .bcftools .boost $(DELLYSOURCES) -- $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) -- --src/cov: .htslib .bcftools .boost $(DELLYSOURCES) -+src/cov: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - --src/dpe: .htslib .bcftools .boost $(DELLYSOURCES) -+src/dpe: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - - clean: - cd src/htslib && make clean - cd src/modular-boost && ./b2 --clean-all -- rm -f $(TARGETS) $(TARGETS:=.o) .htslib .boost .bcftools -+ rm -f $(TARGETS) $(TARGETS:=.o) From 1c0639935809cc64150192517c58d95411748407 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 14:04:37 +0200 Subject: [PATCH 19/58] gnu: diamond: Fetch from git. * gnu/packages/bioinformatics.scm (diamond)[source]: Fetch from git. --- gnu/packages/bioinformatics.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 78debbc873..35611f7b1c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2204,14 +2204,14 @@ (define-public diamond (name "diamond") (version "0.9.22") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/bbuchfink/diamond/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/bbuchfink/diamond.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0adp87r9ak63frdrdmrdfhsn6g0jnnyq1lr2wibvqbxcl37iir9m")))) + "0bky78v79g3wmdpsd706cscckgw1v09fg8vdd0z8z0d5b97aj9zl")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target From 49b2e86adf2b0788c627120ae4c3cf55d3eb9afa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 20:51:02 +0200 Subject: [PATCH 20/58] gnu: Add texlive-latex-doi. * gnu/packages/tex.scm (texlive-latex-doi): New variable. --- gnu/packages/tex.scm | 40 +++++++++++++++++++++++++++++++++++++++- 1 file changed, 39 insertions(+), 1 deletion(-) diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 6a76cbf866..e4c307e54f 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2016, 2018 Efraim Flashner ;;; Copyright © 2016 Federico Beffa ;;; Copyright © 2016 Thomas Danckaert -;;; Copyright © 2016, 2017 Ricardo Wurmus +;;; Copyright © 2016, 2017, 2018 Ricardo Wurmus ;;; Copyright © 2017 Leo Famulari ;;; Copyright © 2017 Marius Bakke ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice @@ -2274,6 +2274,44 @@ (define-public texlive-latex-capt-of to something that's not a float.") (license license:lppl))) +(define-public texlive-latex-doi + (package + (name "texlive-latex-doi") + (version (number->string %texlive-revision)) + (source (origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "svn://www.tug.org/texlive/tags/" + %texlive-tag "/Master/texmf-dist/" + "/tex/latex/doi")) + (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0378rdmrgr2lzbfi4qqy4dfpj5im20diyd8z8b9m4mlg05r7wgnb")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let ((target (string-append (assoc-ref %outputs "out") + "/share/texmf-dist/tex/latex/doi"))) + (mkdir-p target) + (copy-recursively (assoc-ref %build-inputs "source") target) + #t)))) + (home-page "https://www.ctan.org/pkg/doi") + (synopsis "Create correct hyperlinks for DOI numbers") + (description + "You can hyperlink DOI numbers to doi.org. However, some publishers have +elected to use nasty characters in their DOI numbering scheme (@code{<}, +@code{>}, @code{_} and @code{;} have all been spotted). This will either +upset LaTeX, or your PDF reader. This package contains a single user-level +command @code{\\doi{}}, which takes a DOI number, and creates a correct +hyperlink to the target of the DOI.") + ;; Any version of the LPPL. + (license license:lppl1.3+))) + (define-public texlive-latex-etoolbox (package (name "texlive-latex-etoolbox") From 893fbf1285fe2298366a5f1631a191e5daccf3d0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 20:51:27 +0200 Subject: [PATCH 21/58] gnu: Add texlive-generic-listofitems. * gnu/packages/tex.scm (texlive-generic-listofitems): New variable. --- gnu/packages/tex.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index e4c307e54f..8994349e3d 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -4775,3 +4775,37 @@ (define-public texlive-latex-koma-script refers to the version of scrbook, scrreprt, scrartcl, scrlttr2 and typearea (which are the main parts of the bundle).") (license license:lppl1.3+))) + +(define-public texlive-generic-listofitems + (package + (name "texlive-generic-listofitems") + (version (number->string %texlive-revision)) + (source (origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "svn://www.tug.org/texlive/tags/" + %texlive-tag "/Master/texmf-dist/" + "/tex/generic/listofitems")) + (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1k50z6ixgwwzy84mi0dr5vcjah5p7wvgq66y45bilm91a4m8sgla")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let ((target (string-append (assoc-ref %outputs "out") + "/share/texmf-dist/tex/generic/listofitems"))) + (mkdir-p target) + (copy-recursively (assoc-ref %build-inputs "source") target) + #t)))) + (home-page "https://www.ctan.org/pkg/listofitems") + (synopsis "Grab items in lists using user-specified seperation character") + (description + "This package allows one to capture all the items of a list, for which +the parsing character has been selected by the user, and to access any of +these items with a simple syntax.") + (license license:lppl1.3c+))) From 1d0669f4b4658d2d9bef7cf38366099dee40d272 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 20:51:54 +0200 Subject: [PATCH 22/58] gnu: Add texlive-latex-readarray. * gnu/packages/tex.scm (texlive-latex-readarray): New variable. --- gnu/packages/tex.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 8994349e3d..e796fe4c88 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -4809,3 +4809,40 @@ (define-public texlive-generic-listofitems the parsing character has been selected by the user, and to access any of these items with a simple syntax.") (license license:lppl1.3c+))) + +(define-public texlive-latex-readarray + (package + (name "texlive-latex-readarray") + (version (number->string %texlive-revision)) + (source (origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "svn://www.tug.org/texlive/tags/" + %texlive-tag "/Master/texmf-dist/" + "/tex/latex/readarray")) + (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0c53k180ivn1n7fz3ngvd2w1i5dw3kxml0n64vhki88xsylz7lxp")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let ((target (string-append (assoc-ref %outputs "out") + "/share/texmf-dist/tex/latex/readarray"))) + (mkdir-p target) + (copy-recursively (assoc-ref %build-inputs "source") target) + #t)))) + (propagated-inputs + `(("texlive-generic-listofitems" ,texlive-generic-listofitems))) + (home-page "https://www.ctan.org/pkg/readarray") + (synopsis "Read, store and recall array-formatted data") + (description + "This package allows the user to input formatted data into elements of a +2-D or 3-D array and to recall that data at will by individual cell number. +The data can be but need not be numerical in nature. It can be, for example, +formatted text.") + (license license:lppl1.3))) From f50f343e0d138adb328132fb6e17f170261b8798 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 20:52:07 +0200 Subject: [PATCH 23/58] gnu: Add texlive-latex-verbatimbox. * gnu/packages/tex.scm (texlive-latex-verbatimbox): New variable. --- gnu/packages/tex.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index e796fe4c88..46f013b7db 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -4846,3 +4846,42 @@ (define-public texlive-latex-readarray The data can be but need not be numerical in nature. It can be, for example, formatted text.") (license license:lppl1.3))) + +(define-public texlive-latex-verbatimbox + (package + (name "texlive-latex-verbatimbox") + (version (number->string %texlive-revision)) + (source (origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "svn://www.tug.org/texlive/tags/" + %texlive-tag "/Master/texmf-dist/" + "/tex/latex/verbatimbox")) + (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0qh1cgvfs463zsi2pjg490gj0mkjfdpfc381j10cbb5la304psna")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let ((target (string-append (assoc-ref %outputs "out") + "/share/texmf-dist/tex/latex/verbatimbox"))) + (mkdir-p target) + (copy-recursively (assoc-ref %build-inputs "source") target) + #t)))) + (propagated-inputs + `(("texlive-latex-readarray" ,texlive-latex-readarray))) + (home-page "https://www.ctan.org/pkg/verbatimbox") + (synopsis "Deposit verbatim text in a box") + (description + "The package provides a @code{verbbox} environment to place its contents +into a globally available box, or into a box specified by the user. The +global box may then be used in a variety of situations (for example, providing +a replica of the @code{boxedverbatim} environment itself). A valuable use is +in places where the standard @code{verbatim} environment (which is based on a +@code{trivlist}) may not appear.") + (license license:lppl1.3+))) From 4348a059e527969b55875ad33525d6023cd82201 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 20:53:20 +0200 Subject: [PATCH 24/58] gnu: Add texlive-latex-examplep. * gnu/packages/tex.scm (texlive-latex-examplep): New variable. --- gnu/packages/tex.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 46f013b7db..f8b11f7e1a 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -4885,3 +4885,44 @@ (define-public texlive-latex-verbatimbox in places where the standard @code{verbatim} environment (which is based on a @code{trivlist}) may not appear.") (license license:lppl1.3+))) + +(define-public texlive-latex-examplep + (package + (name "texlive-latex-examplep") + (version (number->string %texlive-revision)) + (source (origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "svn://www.tug.org/texlive/tags/" + %texlive-tag "/Master/texmf-dist/" + "/tex/latex/examplep")) + (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0fsvvmz68ij0zwfzrny6x13d92grxr4ap59lxgah4smbkccd6s27")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let ((target (string-append (assoc-ref %outputs "out") + "/share/texmf-dist/tex/latex/examplep"))) + (mkdir-p target) + (copy-recursively (assoc-ref %build-inputs "source") target) + #t)))) + (home-page "https://www.ctan.org/pkg/examplep") + (synopsis "Verbatim phrases and listings in LaTeX") + (description + "Examplep provides sophisticated features for typesetting verbatim source +code listings, including the display of the source code and its compiled LaTeX +or METAPOST output side-by-side, with automatic width detection and enabled +page breaks (in the source), without the need for specifying the source twice. +Special care is taken that section, page and footnote numbers do not interfere +with the main document. For typesetting short verbatim phrases, a replacement +for the @code{\\verb} command is also provided in the package, which can be +used inside tables and moving arguments such as footnotes and section +titles.") + ;; No version of the GPL is specified. + (license license:gpl3+))) From 5748fe5fccef9653ed1e16f83d0fe3e889de6a26 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 20:53:40 +0200 Subject: [PATCH 25/58] gnu: discrover: Fetch from git. * gnu/packages/bioinformatics.scm (discrover)[source]: Fetch from git. --- gnu/packages/bioinformatics.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 35611f7b1c..b6bd2c619a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2239,13 +2239,14 @@ (define-public discrover (version "1.6.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/maaskola/discrover/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/maaskola/discrover.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0rah9ja4m0rl5mldd6vag9rwrivw1zrqxssfq8qx64m7961fp68k")))) + "173fwi2vb6a5kp406hm3jj6j7v4whww796f2qcygp4rpvamh307y")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; there are no tests From 949fa34b84ce8c8027e568878db648c20ff37a5c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 20:58:45 +0200 Subject: [PATCH 26/58] gnu: eigensoft: Update to 7.2.1. * gnu/packages/bioinformatics.scm (eigensoft): Update to 7.2.1. [arguments]: Remove Makefile modification. --- gnu/packages/bioinformatics.scm | 113 +++++++++++++++----------------- 1 file changed, 52 insertions(+), 61 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b6bd2c619a..d0f4429a4c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2274,72 +2274,63 @@ (define-public discrover (license license:gpl3+))) (define-public eigensoft - (let ((revision "1") - (commit "b14d1e202e21e532536ff8004f0419cd5e259dc7")) - (package - (name "eigensoft") - (version (string-append "6.1.2-" - revision "." - (string-take commit 9))) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/DReichLab/EIG.git") - (commit commit))) - (file-name (string-append "eigensoft-" commit "-checkout")) - (sha256 - (base32 - "0f5m6k2j5c16xc3xbywcs989xyc26ncy1zfzp9j9n55n9r4xcaiq")) - (modules '((guix build utils))) - ;; Remove pre-built binaries. - (snippet '(begin - (delete-file-recursively "bin") - (mkdir "bin") - #t)))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; There are no tests. - #:make-flags '("CC=gcc") - #:phases - (modify-phases %standard-phases - ;; There is no configure phase, but the Makefile is in a - ;; sub-directory. - (replace 'configure - (lambda _ - (chdir "src") - ;; The link flags are incomplete. - (substitute* "Makefile" - (("-lgsl") "-lgsl -lm -llapack -llapacke -lpthread")) - #t)) - ;; The provided install target only copies executables to - ;; the "bin" directory in the build root. - (add-after 'install 'actually-install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) - (for-each (lambda (file) - (install-file file bin)) - (find-files "../bin" ".*")) - #t)))))) - (inputs - `(("gsl" ,gsl) - ("lapack" ,lapack) - ("openblas" ,openblas) - ("perl" ,perl) - ("gfortran" ,gfortran "lib"))) - (home-page "https://github.com/DReichLab/EIG") - (synopsis "Tools for population genetics") - (description "The EIGENSOFT package provides tools for population + (package + (name "eigensoft") + (version "7.2.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/DReichLab/EIG.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1c141fqvhnzibmnf22sv23vbmzm20kjjyrib44cfh75wyndp2d9k")) + (modules '((guix build utils))) + ;; Remove pre-built binaries. + (snippet '(begin + (delete-file-recursively "bin") + (mkdir "bin") + #t)))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests. + #:make-flags '("CC=gcc") + #:phases + (modify-phases %standard-phases + ;; There is no configure phase, but the Makefile is in a + ;; sub-directory. + (replace 'configure + (lambda _ (chdir "src") #t)) + ;; The provided install target only copies executables to + ;; the "bin" directory in the build root. + (add-after 'install 'actually-install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (for-each (lambda (file) + (install-file file bin)) + (find-files "../bin" ".*")) + #t)))))) + (inputs + `(("gsl" ,gsl) + ("lapack" ,lapack) + ("openblas" ,openblas) + ("perl" ,perl) + ("gfortran" ,gfortran "lib"))) + (home-page "https://github.com/DReichLab/EIG") + (synopsis "Tools for population genetics") + (description "The EIGENSOFT package provides tools for population genetics and stratification correction. EIGENSOFT implements methods commonly used in population genetics analyses such as PCA, computation of Tracy-Widom statistics, and finding related individuals in structured populations. It comes with a built-in plotting script and supports multiple file formats and quantitative phenotypes.") - ;; The license of the eigensoft tools is Expat, but since it's - ;; linking with the GNU Scientific Library (GSL) the effective - ;; license is the GPL. - (license license:gpl3+)))) + ;; The license of the eigensoft tools is Expat, but since it's + ;; linking with the GNU Scientific Library (GSL) the effective + ;; license is the GPL. + (license license:gpl3+))) (define-public edirect (package From c96ca68f31619ed678720fc1dc6bbf0906ce5638 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 21:11:37 +0200 Subject: [PATCH 27/58] gnu: edirect: Update to 10.2.20181018. * gnu/packages/bioinformatics.scm (edirect): Update to 10.2.20181018. [arguments]: Add simple check phase; simplify other phases. [inputs]: Add perl-xml-simple. --- gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++-------------- 1 file changed, 26 insertions(+), 20 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d0f4429a4c..a806fd5f22 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2335,36 +2335,41 @@ (define-public eigensoft (define-public edirect (package (name "edirect") - (version "4.10") + (version "10.2.20181018") (source (origin (method url-fetch) - (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/" - "versions/2016-05-03/edirect.tar.gz")) + (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect" + "/versions/" version + "/edirect-" version ".tar.gz")) (sha256 (base32 - "15zsprak5yh8c1yrz4r1knmb5s8qcmdid4xdhkh3lqcv64l60hli")))) + "091f4aigzpbqih6h82nq566gkp3y07i72yqndmqskfgar1vwgci7")))) (build-system perl-build-system) (arguments - `(#:tests? #f ;no "check" target - #:phases + `(#:phases (modify-phases %standard-phases (delete 'configure) (delete 'build) + (delete 'check) ; simple check after install (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((target (string-append (assoc-ref outputs "out") - "/bin"))) - (mkdir-p target) - (install-file "edirect.pl" target) - #t))) - (add-after - 'install 'wrap-program - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Make sure 'edirect.pl' finds all perl inputs at runtime. - (let* ((out (assoc-ref outputs "out")) - (path (getenv "PERL5LIB"))) - (wrap-program (string-append out "/bin/edirect.pl") - `("PERL5LIB" ":" prefix (,path))))))))) + (lambda* (#:key outputs #:allow-other-keys) + (install-file "edirect.pl" + (string-append (assoc-ref outputs "out") "/bin")) + #t)) + (add-after 'install 'wrap-program + (lambda* (#:key outputs #:allow-other-keys) + ;; Make sure 'edirect.pl' finds all perl inputs at runtime. + (let* ((out (assoc-ref outputs "out")) + (path (getenv "PERL5LIB"))) + (wrap-program (string-append out "/bin/edirect.pl") + `("PERL5LIB" ":" prefix (,path)))) + #t)) + (add-after 'wrap-program 'check + (lambda* (#:key outputs #:allow-other-keys) + (invoke (string-append (assoc-ref outputs "out") + "/bin/edirect.pl") + "-filter" "-help") + #t))))) (inputs `(("perl-html-parser" ,perl-html-parser) ("perl-encode-locale" ,perl-encode-locale) @@ -2380,6 +2385,7 @@ (define-public edirect ("perl-net-http" ,perl-net-http) ("perl-uri" ,perl-uri) ("perl-www-robotrules" ,perl-www-robotrules) + ("perl-xml-simple" ,perl-xml-simple) ("perl" ,perl))) (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/") (synopsis "Tools for accessing the NCBI's set of databases") From 38622ccd14c5d2df152ff8d72f1f5269afb36565 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 21:26:35 +0200 Subject: [PATCH 28/58] gnu: express-beta-diversity: Update to 1.0.8. * gnu/packages/bioinformatics.scm (express-beta-diversity): Update to 1.0.8. [source]: Fetch from git. [arguments]: Use INVOKE; remove "exit-source" build phase; simplify. --- gnu/packages/bioinformatics.scm | 31 +++++++++++++------------------ 1 file changed, 13 insertions(+), 18 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a806fd5f22..9a04118588 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2481,17 +2481,16 @@ (define-public express (define-public express-beta-diversity (package (name "express-beta-diversity") - (version "1.0.7") + (version "1.0.8") (source (origin - (method url-fetch) - (uri - (string-append - "https://github.com/dparks1134/ExpressBetaDiversity/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/dparks1134/ExpressBetaDiversity.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr")))) + "0s0yzg5c21349rh7x4w9266jsvnp7j1hp9cf8sk32hz8nvrj745x")))) (build-system gnu-build-system) (arguments `(#:phases @@ -2499,17 +2498,13 @@ (define-public express-beta-diversity (delete 'configure) (add-before 'build 'enter-source (lambda _ (chdir "source") #t)) (replace 'check - (lambda _ (zero? (system* "../bin/ExpressBetaDiversity" - "-u")))) - (add-after 'check 'exit-source (lambda _ (chdir "..") #t)) + (lambda _ (invoke "../bin/ExpressBetaDiversity" "-u") #t)) (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") - "/bin"))) - (mkdir-p bin) - (install-file "scripts/convertToEBD.py" bin) - (install-file "bin/ExpressBetaDiversity" bin) - #t)))))) + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "../scripts/convertToEBD.py" bin) + (install-file "../bin/ExpressBetaDiversity" bin) + #t)))))) (inputs `(("python" ,python-2))) (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity") From 0db75f7a79126a368e0c8fb2d71abf76da065a3f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 21:30:53 +0200 Subject: [PATCH 29/58] gnu: fasttree: Use INVOKE. * gnu/packages/bioinformatics.scm (fasttree)[arguments]: Use INVOKE; simplify install phase. --- gnu/packages/bioinformatics.scm | 45 ++++++++++++++++----------------- 1 file changed, 22 insertions(+), 23 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9a04118588..a99deeb0a6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2537,31 +2537,30 @@ (define-public fasttree (delete 'configure) (replace 'build (lambda* (#:key source #:allow-other-keys) - (and (zero? (system* "gcc" - "-O3" - "-finline-functions" - "-funroll-loops" - "-Wall" - "-o" - "FastTree" - source - "-lm")) - (zero? (system* "gcc" - "-DOPENMP" - "-fopenmp" - "-O3" - "-finline-functions" - "-funroll-loops" - "-Wall" - "-o" - "FastTreeMP" - source - "-lm"))))) + (invoke "gcc" + "-O3" + "-finline-functions" + "-funroll-loops" + "-Wall" + "-o" + "FastTree" + source + "-lm") + (invoke "gcc" + "-DOPENMP" + "-fopenmp" + "-O3" + "-finline-functions" + "-funroll-loops" + "-Wall" + "-o" + "FastTreeMP" + source + "-lm") + #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") - "/bin"))) - (mkdir-p bin) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (install-file "FastTree" bin) (install-file "FastTreeMP" bin) #t)))))) From 50e33c3a8c591af8a6112ea42d53ed6f0ec80208 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 22:58:30 +0200 Subject: [PATCH 30/58] gnu: python-screed: Update to 1.0. * gnu/packages/bioinformatics.scm (python-screed): Update to 1.0. [arguments]: Run tests after installation. [native-inputs]: Add python-pytest, python-pytest-cov, and python-pytest-runner; remove python-nose. --- gnu/packages/bioinformatics.scm | 31 ++++++++++++++++++++++--------- 1 file changed, 22 insertions(+), 9 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a99deeb0a6..9afb2c1197 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5602,25 +5602,38 @@ (define-public preseq (define-public python-screed (package (name "python-screed") - (version "0.9") + (version "1.0") (source (origin (method url-fetch) (uri (pypi-uri "screed" version)) (sha256 (base32 - "18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0")))) + "148vcb7w2wr6a4w6vs2bsxanbqibxfk490zbcbg4m61s8669zdjx")))) (build-system python-build-system) (arguments - `(#:phases + '(#:phases (modify-phases %standard-phases - (replace 'check - (lambda _ - (setenv "PYTHONPATH" - (string-append (getenv "PYTHONPATH") ":.")) - (zero? (system* "nosetests" "--attr" "!known_failing"))))))) + ;; Tests must be run after installation, as the "screed" command does + ;; not exist right after building. + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (setenv "PYTHONPATH" + (string-append out "/lib/python" + (string-take (string-take-right + (assoc-ref inputs "python") + 5) 3) + "/site-packages:" + (getenv "PYTHONPATH"))) + (setenv "PATH" (string-append out "/bin:" (getenv "PATH")))) + (invoke "python" "setup.py" "test") + #t))))) (native-inputs - `(("python-nose" ,python-nose))) + `(("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-runner" ,python-pytest-runner))) (inputs `(("python-bz2file" ,python-bz2file))) (home-page "https://github.com/dib-lab/screed/") From 4b8f4536ce6107bf3417252b2206d14912399344 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 22:59:37 +0200 Subject: [PATCH 31/58] gnu: khmer: Update to 2.1.2. * gnu/packages/bioinformatics.scm (khmer): Update to 2.1.2. [source]: Fetch from git; remove bundled libraries in snippet. [arguments]: Remove "set-paths" phase; remove "post-install-check" phase; remove "reset-gzip-timestamps" phase. [native-inputs]: Remove seqan and python-nose; add python-cython, python-pytest, and python-pytest-runner. [inputs]: Remove gcc-4.9. --- gnu/packages/bioinformatics.scm | 83 +++++++++++---------------------- 1 file changed, 28 insertions(+), 55 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9afb2c1197..9163b5dc8a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3742,75 +3742,48 @@ (define-public jellyfish (define-public khmer (package (name "khmer") - (version "2.0") + (version "2.1.2") (source (origin - (method url-fetch) - (uri (pypi-uri "khmer" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/dib-lab/khmer.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0wb05shqh77v00256qlm68vbbx3kl76fyzihszbz5nhanl4ni33a")) - (patches (search-patches "khmer-use-libraries.patch")))) + "02x38d9jw2r58y8dmnj4hffy9wxv1yc1jwbvdbhby9dxndv94r9m")) + (patches (search-patches "khmer-use-libraries.patch")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete bundled libraries. We do not replace the bundled seqan + ;; as it is a modified subset of the old version 1.4.1. + ;; + ;; We do not replace the bundled MurmurHash as the canonical + ;; repository for this code 'SMHasher' is unsuitable for providing + ;; a library. See + ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html + (delete-file-recursively "third-party/zlib") + (delete-file-recursively "third-party/bzip2") + #t)))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'set-paths - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Delete bundled libraries. - (delete-file-recursively "third-party/zlib") - (delete-file-recursively "third-party/bzip2") - ;; Replace bundled seqan. - (let* ((seqan-all "third-party/seqan") - (seqan-include (string-append - seqan-all "/core/include"))) - (delete-file-recursively seqan-all) - (copy-recursively (string-append (assoc-ref inputs "seqan") - "/include/seqan") - (string-append seqan-include "/seqan"))) - ;; We do not replace the bundled MurmurHash as the canonical - ;; repository for this code 'SMHasher' is unsuitable for - ;; providing a library. See - ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html - #t)) (add-after 'unpack 'set-cc - (lambda _ - (setenv "CC" "gcc") - #t)) - ;; It is simpler to test after installation. - (delete 'check) - (add-after 'install 'post-install-check - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (setenv "PATH" - (string-append - (getenv "PATH") - ":" - (assoc-ref outputs "out") - "/bin")) - (setenv "PYTHONPATH" - (string-append - (getenv "PYTHONPATH") - ":" - out - "/lib/python" - (string-take (string-take-right - (assoc-ref inputs "python") 5) 3) - "/site-packages")) - (with-directory-excursion "build" - (zero? (system* "nosetests" "khmer" "--attr" - "!known_failing"))))))))) + (lambda _ (setenv "CC" "gcc") #t)) + ;; FIXME: This fails with "permission denied". + (delete 'reset-gzip-timestamps)))) (native-inputs - `(("seqan" ,seqan) - ("python-nose" ,python-nose))) + `(("python-cython" ,python-cython) + ("python-pytest" ,python-pytest) + ("python-pytest-runner" ,python-pytest-runner))) (inputs `(("zlib" ,zlib) ("bzip2" ,bzip2) ("python-screed" ,python-screed) - ("python-bz2file" ,python-bz2file) - ;; Tests fail when gcc-5 is used for compilation. Use gcc-4.9 at least - ;; until the next version of khmer (likely 2.1) is released. - ("gcc" ,gcc-4.9))) + ("python-bz2file" ,python-bz2file))) (home-page "https://khmer.readthedocs.org/") (synopsis "K-mer counting, filtering and graph traversal library") (description "The khmer software is a set of command-line tools for From 4d93a9a36c3ddc431789fa38201b0fd657412dbe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 23:03:57 +0200 Subject: [PATCH 32/58] gnu: seqan: Update to 2.4.0. * gnu/packages/bioinformatics.scm (seqan): Update to 2.4.0. [native-inputs]: Replace bzip2 with xz. (seqan-1): New variable. (tophat)[inputs]: Use seqan-1. --- gnu/packages/bioinformatics.scm | 58 ++++++++++++++++++++++++++------- 1 file changed, 47 insertions(+), 11 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9163b5dc8a..cdb82aee8b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1382,7 +1382,7 @@ (define-public tophat ("python" ,python-2) ("perl" ,perl) ("zlib" ,zlib) - ("seqan" ,seqan))) + ("seqan" ,seqan-1))) (home-page "http://ccb.jhu.edu/software/tophat/index.shtml") (synopsis "Spliced read mapper for RNA-Seq data") (description @@ -5732,6 +5732,51 @@ (define-public sra-tools (define-public seqan (package + (name "seqan") + (version "2.4.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/seqan/seqan/releases/" + "download/seqan-v" version + "/seqan-library-" version ".tar.xz")) + (sha256 + (base32 + "19a1rlxx03qy1i1iriicly68w64yjxbv24g9gdywnfmq998v35yx")))) + ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it + ;; makes sense to split the outputs. + (outputs '("out" "doc")) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let ((tar (assoc-ref %build-inputs "tar")) + (xz (assoc-ref %build-inputs "xz")) + (out (assoc-ref %outputs "out")) + (doc (assoc-ref %outputs "doc"))) + (setenv "PATH" (string-append tar "/bin:" xz "/bin")) + (invoke "tar" "xvf" (assoc-ref %build-inputs "source")) + (chdir (string-append "seqan-library-" ,version)) + (copy-recursively "include" (string-append out "/include")) + (copy-recursively "share" (string-append doc "/share")) + #t)))) + (native-inputs + `(("source" ,source) + ("tar" ,tar) + ("xz" ,xz))) + (home-page "http://www.seqan.de") + (synopsis "Library for nucleotide sequence analysis") + (description + "SeqAn is a C++ library of efficient algorithms and data structures for +the analysis of sequences with the focus on biological data. It contains +algorithms and data structures for string representation and their +manipulation, online and indexed string search, efficient I/O of +bioinformatics file formats, sequence alignment, and more.") + (license license:bsd-3))) + +(define-public seqan-1 + (package (inherit seqan) (name "seqan") (version "1.4.2") (source (origin @@ -5763,16 +5808,7 @@ (define-public seqan (native-inputs `(("source" ,source) ("tar" ,tar) - ("bzip2" ,bzip2))) - (home-page "http://www.seqan.de") - (synopsis "Library for nucleotide sequence analysis") - (description - "SeqAn is a C++ library of efficient algorithms and data structures for -the analysis of sequences with the focus on biological data. It contains -algorithms and data structures for string representation and their -manipulation, online and indexed string search, efficient I/O of -bioinformatics file formats, sequence alignment, and more.") - (license license:bsd-3))) + ("bzip2" ,bzip2))))) (define-public seqmagick (package From f8ee22fc8b486612a9f041bb351d99ba0ce16dc0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 23:05:11 +0200 Subject: [PATCH 33/58] gnu: flexbar: Update to 3.4.0. * gnu/packages/bioinformatics.scm (flexbar): Update to 3.4.0. [source]: Fetch from git. [arguments]: Adjust check and install phases. [home-page]: Update to new home at Github. [license]: Change to bsd-3. --- gnu/packages/bioinformatics.scm | 39 +++++++++++++++++---------------- 1 file changed, 20 insertions(+), 19 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cdb82aee8b..96ea07bdc4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2607,38 +2607,39 @@ (define-public fastx-toolkit (define-public flexbar (package (name "flexbar") - (version "2.5") + (version "3.4.0") (source (origin - (method url-fetch) - (uri - (string-append "mirror://sourceforge/flexbar/" - version "/flexbar_v" version "_src.tgz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/seqan/flexbar.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf")))) + "1pq9sxvdnldl14libk234m72dqhwgzs3acgl943wchwdqlcsi5r2")))) (build-system cmake-build-system) (arguments - `(#:configure-flags (list - (string-append "-DFLEXBAR_BINARY_DIR=" - (assoc-ref %outputs "out") - "/bin/")) - #:phases + `(#:phases (modify-phases %standard-phases (replace 'check (lambda* (#:key outputs #:allow-other-keys) - (setenv "PATH" (string-append - (assoc-ref outputs "out") "/bin:" - (getenv "PATH"))) - (chdir "../flexbar_v2.5_src/test") - (zero? (system* "bash" "flexbar_validate.sh")))) - (delete 'install)))) + (setenv "PATH" (string-append (getcwd) ":" (getenv "PATH"))) + (with-directory-excursion "../source/test" + (invoke "bash" "flexbar_test.sh")) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (string-append (assoc-ref outputs "out"))) + (bin (string-append out "/bin/"))) + (install-file "flexbar" bin)) + #t))))) (inputs `(("tbb" ,tbb) ("zlib" ,zlib))) (native-inputs `(("pkg-config" ,pkg-config) ("seqan" ,seqan))) - (home-page "http://flexbar.sourceforge.net") + (home-page "https://github.com/seqan/flexbar") (synopsis "Barcode and adapter removal tool for sequencing platforms") (description "Flexbar preprocesses high-throughput nucleotide sequencing data @@ -2647,7 +2648,7 @@ (define-public flexbar read mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform.") - (license license:gpl3))) + (license license:bsd-3))) (define-public fraggenescan (package From aff38cb199fc847f97059600a6c9c99ee754fc07 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 20 Oct 2018 17:39:53 +0200 Subject: [PATCH 34/58] =?UTF-8?q?install:=20Make=20/var/guix/=E2=80=A6/gui?= =?UTF-8?q?x-profile=20a=20relative=20symlink.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/build/install.scm (populate-single-profile-directory): Make /var/guix/profiles/per-user/root/guix-profile a relative symlink. --- gnu/build/install.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/build/install.scm b/gnu/build/install.scm index 5a5e703872..c602d69489 100644 --- a/gnu/build/install.scm +++ b/gnu/build/install.scm @@ -199,7 +199,7 @@ (define (symlink* old new) (mkdir-p* %root-profile) (symlink* profile (string-append %root-profile "/guix-profile-1-link")) - (symlink* (string-append %root-profile "/guix-profile-1-link") + (symlink* "guix-profile-1-link" (string-append %root-profile "/guix-profile")) (mkdir-p* "/root") From 16d212510aa597639ffe5a847503a07170e239cd Mon Sep 17 00:00:00 2001 From: Luther Thompson Date: Sun, 21 Oct 2018 23:45:52 +0200 Subject: [PATCH 35/58] gnu: Add python-ilinkedlist. * gnu/packages/python.scm (python-ilinkedlist): New variable. --- gnu/packages/python.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 29ce213afb..9c749227de 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -55,6 +55,7 @@ ;;; Copyright © 2018 Oleg Pykhalov ;;; Copyright © 2018 Clément Lassieur ;;; Copyright © 2018 Maxim Cournoyer +;;; Copyright © 2018 Luther Thompson ;;; ;;; This file is part of GNU Guix. ;;; @@ -14504,3 +14505,28 @@ (define-public python-dask larger-than-memory or distributed environments. These parallel collections run on top of the dynamic task schedulers. ") (license license:bsd-3))) + +(define-public python-ilinkedlist + (package + (name "python-ilinkedlist") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ilinkedlist" version)) + (sha256 + (base32 + "063c2gm4jkgkv0nsg7mrc8y0w82ms98l4xchmbrvr68cscglhk69")))) + (build-system python-build-system) + (native-inputs `(("python-pytest" ,python-pytest))) + (inputs `(("python" ,python))) + (home-page "https://github.com/luther9/ilinkedlist-py") + (synopsis "Immutable linked list library") + (description + "This is a implementation of immutable linked lists for Python. It +contains @code{nil} (the empty linked list) and a @code{Pair} class for nodes. +Since a linked list is treated as immutable, it is hashable, and its length +can be retrieved in constant time. Some of the terminology is inspired by +LISP. It is possible to create an improper list by creating a @code{Pair} +with a non-list @code{cdr}.") + (license license:gpl3+))) From ff598353c01b1953243ba0ecb87efbd73c66720e Mon Sep 17 00:00:00 2001 From: Pierre Langlois Date: Sat, 20 Oct 2018 11:17:24 +0100 Subject: [PATCH 36/58] gnu: light: Update to 1.2. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/linux.scm (light): Update to 1.2. [source]: Switch to url-fetch. [arguments]: Remove. [native-inputs]: Remove help2man. Add autoconf and automake. Signed-off-by: Ludovic Courtès --- gnu/packages/linux.scm | 30 +++++++++++------------------- 1 file changed, 11 insertions(+), 19 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index bc53a88bfc..2c6bd79231 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -30,6 +30,7 @@ ;;; Copyright © 2018 Pierre-Antoine Rouby ;;; Copyright © 2018 Brendan Tildesley ;;; Copyright © 2018 Manuel Graf +;;; Copyright © 2018 Pierre Langlois ;;; ;;; This file is part of GNU Guix. ;;; @@ -4167,30 +4168,21 @@ (define-public sysstat (define-public light (package (name "light") - (version "1.1.2") + (version "1.2") (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/haikarainen/light") - (commit version))) + (method url-fetch) + (uri (string-append + "https://github.com/haikarainen/light/archive/v" + version ".tar.gz")) (sha256 (base32 - "0c934gxav9cgdf94li6dp0rfqmpday9d33vdn9xb2mfp4war9n4w")))) + "1gfvsw7gh5pis733l7j54vzp272pvjyzbg8a0pvapfmg0s7mip97")) + (file-name (string-append name "-" version ".tar.gz")))) (build-system gnu-build-system) - (arguments - '(#:tests? #f ; no tests - #:make-flags (list "CC=gcc" - (string-append "PREFIX=" %output)) - #:phases - (modify-phases %standard-phases - (delete 'configure) ; no configure script - (add-after 'unpack 'patch-makefile - (lambda _ - (substitute* "Makefile" (("chown") "#")) - #t))))) (native-inputs - `(("help2man" ,help2man))) - (home-page "https://haikarainen.github.io/light") + `(("autoconf" ,autoconf) + ("automake" ,automake))) + (home-page "https://haikarainen.github.io/light/") (synopsis "GNU/Linux application to control backlights") (description "Light is a program to send commands to screen backlight controllers From df71447e992e82d029ac57d0d721af02fc6a5061 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 20 Oct 2018 12:26:51 -0400 Subject: [PATCH 37/58] gnu: OpenSSH: Update to 7.9p1. * gnu/packages/ssh.scm (openssh): Update to 7.9p1. --- gnu/packages/ssh.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ssh.scm b/gnu/packages/ssh.scm index 829977f5c5..e806fc80f2 100644 --- a/gnu/packages/ssh.scm +++ b/gnu/packages/ssh.scm @@ -147,14 +147,14 @@ (define-public libssh2 (define-public openssh (package (name "openssh") - (version "7.8p1") + (version "7.9p1") (source (origin (method url-fetch) (uri (string-append "mirror://openbsd/OpenSSH/portable/" name "-" version ".tar.gz")) (sha256 (base32 - "1jj4f586r9lhakp2w0zv7j616d6x62m15q8l4nxq7haja6qlnj0s")))) + "1b8sy6v0b8v4ggmknwcqx3y1rjcpsll0f1f8f4vyv11x4ni3njvb")))) (build-system gnu-build-system) (native-inputs `(("groff" ,groff))) (inputs `(("openssl" ,openssl) From dc3dfa131f97105baefeb34e5155e89946dc1eba Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 22 Oct 2018 00:38:26 +0200 Subject: [PATCH 38/58] gnu: knot: Update to 2.7.3. * gnu/packages/dns.scm (knot): Update to 2.7.3. --- gnu/packages/dns.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index ad1a8638bc..1dcf73771b 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -569,14 +569,14 @@ (define-public yadifa (define-public knot (package (name "knot") - (version "2.7.2") + (version "2.7.3") (source (origin (method url-fetch) (uri (string-append "https://secure.nic.cz/files/knot-dns/" name "-" version ".tar.xz")) (sha256 (base32 - "0cc4wgb02ch09x99a1fnr7vsdik8k920q7jafzcamjvy3kpb4w6b")) + "1pwjcv7hzhqawisibybma160k77a6f1v94xw6ay9c7j49vrw05w7")) (modules '((guix build utils))) (snippet '(begin From 69c69c2d8e4922ee997f213772acabb95d33a467 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 21 Oct 2018 23:16:50 -0400 Subject: [PATCH 39/58] gnu: libmpdclient: Update to 2.16. * gnu/packages/mpd.scm (libmpdclient): Update to 2.16. --- gnu/packages/mpd.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index 3e69ddba69..b69be2965f 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -58,7 +58,7 @@ (define-module (gnu packages mpd) (define-public libmpdclient (package (name "libmpdclient") - (version "2.15") + (version "2.16") (source (origin (method url-fetch) (uri @@ -67,7 +67,7 @@ (define-public libmpdclient "/libmpdclient-" version ".tar.xz")) (sha256 (base32 - "1la60ar6i4ghpscrlgm45kci9b74bvkpsfybhg0ygs4rzpwzdnxl")))) + "0r24cl3i9nvs6a47mvwaxk1kb5wmnhkhrw1q5cq9010fgjvdlszs")))) (build-system meson-build-system) (native-inputs `(("pkg-config" ,pkg-config) From 318ec0a896dff7f311d67c6ac9f1bea31efb5e3e Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 22 Oct 2018 03:31:51 -0400 Subject: [PATCH 40/58] gnu: livemedia-utils: Update to 2018.10.17 [fixes CVE-2018-4013]. * gnu/packages/video.scm (livemedia-utils): Update to 2018.10.17. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index a6930abfda..4fcd15e4aa 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -2645,7 +2645,7 @@ (define-public mediainfo (define-public livemedia-utils (package (name "livemedia-utils") - (version "2017.10.28") + (version "2018.10.17") (source (origin (method url-fetch) (uri (string-append @@ -2653,7 +2653,7 @@ (define-public livemedia-utils version ".tar.gz")) (sha256 (base32 - "0f5kxpayqn3yhabqrd2cqlc74i6x2xr01jfkank1lcilxnfyrsnq")) + "1s69ipvdc6ldscp0cr1zpsll8xc3qcagr95nl84x7b1rbg4xjs3w")) (modules '((guix build utils))) (snippet '(begin ;; As of glibc 2.26, no longer is. From 09aa3d063a0eacf3fca8d4803fbb62bd7b1ee663 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 22 Oct 2018 13:00:06 +0200 Subject: [PATCH 41/58] gnu: Add r-ruvseq. * gnu/packages/bioconductor.scm (r-ruvseq): New variable. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1b779855b2..92b67453f6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -913,3 +913,29 @@ (define-public r-dnabarcodes barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e. assigned to their original reference barcode.") (license license:gpl2))) + +(define-public r-ruvseq + (package + (name "r-ruvseq") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RUVSeq" version)) + (sha256 + (base32 + "16i5sm5af761k4zvspfi8jknsgln48bn538hxqqmlaq7wvlfxqxj")))) + (properties `((upstream-name . "RUVSeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-edaseq" ,r-edaseq) + ("r-edger" ,r-edger) + ("r-mass" ,r-mass))) + (home-page "https://github.com/drisso/RUVSeq") + (synopsis "Remove unwanted variation from RNA-Seq data") + (description + "This package implements methods to @dfn{remove unwanted variation} (RUV) +of Risso et al. (2014) for the normalization of RNA-Seq read counts between +samples.") + (license license:artistic2.0))) From 3a352a44056f4680bbb1de038bd0292803c35b1e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 22 Oct 2018 15:56:38 +0200 Subject: [PATCH 42/58] gnu: snap: Update to 4.2.2.2. * gnu/packages/education.scm (snap): Update to 4.2.2.2. Update source URL. --- gnu/packages/education.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm index 8b02adc182..b333bb9d35 100644 --- a/gnu/packages/education.scm +++ b/gnu/packages/education.scm @@ -243,17 +243,17 @@ (define-public tipp10 (define-public snap (package (name "snap") - (version "4.2.1.4") + (version "4.2.2.2") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/jmoenig/Snap--Build-Your-Own-Blocks.git") + (url "https://github.com/jmoenig/Snap.git") (commit version))) (file-name (git-file-name name version)) (sha256 (base32 - "0yc0w0cdhvi0nwqqrann2v3y0n7shxh7irgixqvlavp4k49d7aqj")))) + "0bay08yr58qj8wzpjg33gdj78rfhyskfzidknpdl3cr1jrj6i4p9")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -265,7 +265,7 @@ (define-public snap (share (string-append out "/share/snap"))) (copy-recursively source share) ;; Replace the sole minified file in the package. - (with-directory-excursion share + (with-directory-excursion (string-append share "/src") (delete-file "FileSaver.min.js") (symlink (string-append (assoc-ref %build-inputs "js-filesaver") "/share/javascript/FileSaver.min.js") From 51f4e36cb9cc45493397bc799f7a87e5de92560d Mon Sep 17 00:00:00 2001 From: Christopher Lemmer Webber Date: Mon, 22 Oct 2018 09:59:42 -0400 Subject: [PATCH 43/58] gnu: Add emacs-scribble-mode. * gnu/packages/emacs.scm (emacs-scribble-mode): New variable. --- gnu/packages/emacs.scm | 29 ++++++++++++++++++++++++++++- 1 file changed, 28 insertions(+), 1 deletion(-) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 47e984e101..ce98dbaeb8 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2015 Federico Beffa ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018 Chris Marusich -;;; Copyright © 2015, 2016 Christopher Allan Webber +;;; Copyright © 2015, 2016, 2018 Christopher Lemmer Webber ;;; Copyright © 2016 Adriano Peluso ;;; Copyright © 2016, 2017, 2018 Efraim Flashner ;;; Copyright © 2016 David Thompson @@ -654,6 +654,33 @@ (define-public emacs-ghub only a handful of functions that are not resource-specific.") (license license:gpl3+))) +(define-public emacs-scribble-mode + (let ((commit "34e9e5edb921813b6483e0fefa848efb6ee4b314") + (version "0.0") + (revision 0)) + (package + (name "emacs-scribble-mode") + (version (if (zero? revision) + version + (string-append version "-" + (number->string revision) + "." (string-take commit 7)))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emacs-pe/scribble-mode.git") + (commit commit))) + (sha256 + (base32 + "0598byqpz2q6yi2q4dwd77jj9z3n99z34d3an51s9m2za0nh1qvp")))) + (build-system emacs-build-system) + (home-page "https://github.com/emacs-pe/scribble-mode") + (synopsis "Emacs mode for editing the Scribble documentation syntax.") + (description + "This package provides basic syntax highlighting and editing support +for editing Racket's Scribble documentation syntax in Emacs.") + (license license:gpl3+)))) + (define-public emacs-haskell-mode (package (name "emacs-haskell-mode") From 50401c2a6853a65d89ab9be3f24a4f5386e3b684 Mon Sep 17 00:00:00 2001 From: Meiyo Peng Date: Thu, 18 Oct 2018 09:22:36 +0800 Subject: [PATCH 44/58] gnu: libqtxdg: Update to 3.2.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (libqtxdg): Update to 3.2.0. Signed-off-by: 宋文武 --- gnu/packages/lxqt.scm | 33 +++++++++++++++++++++------------ 1 file changed, 21 insertions(+), 12 deletions(-) diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index c84d26d4cb..57dd5b9c2f 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2016 Efraim Flashner ;;; Copyright © 2017 Nils Gillmann ;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2018 Meiyo Peng ;;; ;;; This file is part of GNU Guix. ;;; @@ -36,25 +37,33 @@ (define-module (gnu packages lxqt) (define-public libqtxdg (package (name "libqtxdg") - (version "1.2.0") + (version "3.2.0") (source (origin (method url-fetch) - (uri - (string-append "https://github.com/lxde/libqtxdg/releases/" - "download/" version "/" name "-" version ".tar.xz")) + (uri (string-append + "https://github.com/lxqt/" name "/releases/download/" + version "/" name "-" version ".tar.xz")) (sha256 - (base32 - "1ncqs0lcll5nx69hxfg33m3jfkryjqrjhr2kdci0b8pyaqdv1jc8")))) + (base32 "0lq548pa69hfvnbj2ypba5ygm8n6v6g7bqqm8p5g538l1l3394cl")))) (build-system cmake-build-system) (arguments - `(#:tests? #f ; test fails with message "Exception" - #:configure-flags '("-DBUILD_TESTS=ON"))) - (native-inputs - `(("pkg-config" ,pkg-config))) + `(#:configure-flags + `("-DBUILD_TESTS=ON" + ,(string-append "-DQTXDGX_ICONENGINEPLUGIN_INSTALL_PATH=" + %output "/lib/qt5/plugins/iconengines")) + #:phases + (modify-phases %standard-phases + (add-before 'check 'pre-check + (lambda _ + ;; Run the tests offscreen. + (setenv "QT_QPA_PLATFORM" "offscreen") + #t))))) (propagated-inputs - `(("qtbase" ,qtbase))) ; according to Qt5Xdg.pc - (home-page "https://github.com/lxde/libqtxdg") + ;; required by Qt5XdgIconLoader.pc + `(("qtbase" ,qtbase) + ("qtsvg" ,qtsvg))) + (home-page "https://github.com/lxqt/libqtxdg") (synopsis "Qt implementation of freedesktop.org xdg specifications") (description "Libqtxdg implements the freedesktop.org xdg specifications in Qt.") From 9861bcd182b1ba89a93630a2178b170a088f0a6b Mon Sep 17 00:00:00 2001 From: Meiyo Peng Date: Thu, 18 Oct 2018 10:30:35 +0800 Subject: [PATCH 45/58] gnu: liblxqt: Update to 0.13.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (liblxqt): Update to 0.13.0. [source]: Remove patches. [home-page]: Use HTTPS. * gnu/packages/patches/liblxqt-include.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. Signed-off-by: 宋文武 --- gnu/local.mk | 1 - gnu/packages/lxqt.scm | 39 ++++++++++++++-------- gnu/packages/patches/liblxqt-include.patch | 14 -------- 3 files changed, 26 insertions(+), 28 deletions(-) delete mode 100644 gnu/packages/patches/liblxqt-include.patch diff --git a/gnu/local.mk b/gnu/local.mk index d155b4c613..47883f829e 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -885,7 +885,6 @@ dist_patch_DATA = \ %D%/packages/patches/libjxr-fix-function-signature.patch \ %D%/packages/patches/libjxr-fix-typos.patch \ %D%/packages/patches/libotr-test-auth-fix.patch \ - %D%/packages/patches/liblxqt-include.patch \ %D%/packages/patches/libmad-armv7-thumb-pt1.patch \ %D%/packages/patches/libmad-armv7-thumb-pt2.patch \ %D%/packages/patches/libmad-frame-length.patch \ diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 57dd5b9c2f..c4d0662e99 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -32,7 +32,9 @@ (define-module (gnu packages lxqt) #:use-module (gnu packages glib) #:use-module (gnu packages kde-frameworks) #:use-module (gnu packages pkg-config) - #:use-module (gnu packages qt)) + #:use-module (gnu packages polkit) + #:use-module (gnu packages qt) + #:use-module (gnu packages xorg)) (define-public libqtxdg (package @@ -72,29 +74,40 @@ (define-public libqtxdg (define-public liblxqt (package (name "liblxqt") - (version "0.9.0") + (version "0.13.0") (source (origin (method url-fetch) - (uri - (string-append "https://github.com/lxde/" name - "/archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (uri (string-append + "https://github.com/lxqt/" name "/releases/download/" + version "/" name "-" version ".tar.xz")) (sha256 - (base32 - "0mbl3qc0yfgfsndqrw8vg8k5irsy0pg2wrad8nwv0aphphd4n7rg")) - (patches (search-patches "liblxqt-include.patch")))) + (base32 "0fba0nq5b9fvvmklcikcd4nwhzlp5d6k1q1f80r34kncdzfvj7dl")))) (build-system cmake-build-system) (arguments - `(#:tests? #f)) - (native-inputs `(("pkg-config" ,pkg-config))) + `(#:tests? #f ; no tests + #:configure-flags + ;; TODO: prefetch translations files from 'lxqt-l10n'. + '("-DPULL_TRANSLATIONS=NO") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-source + (lambda _ + (substitute* "CMakeLists.txt" + (("DESTINATION \"\\$\\{POLKITQT-1_POLICY_FILES_INSTALL_DIR\\}") + "DESTINATION \"${CMAKE_INSTALL_PREFIX}/share/polkit-1/actions")) + #t))))) (inputs `(("kwindowsystem" ,kwindowsystem) ("libqtxdg" ,libqtxdg) - ("qtbase" ,qtbase) + ("libxscrnsaver" ,libxscrnsaver) + ("polkit-qt" ,polkit-qt) + ("qtsvg" ,qtsvg) ("qttools" ,qttools) ("qtx11extras" ,qtx11extras))) - (home-page "http://lxqt.org/") + (native-inputs + `(("lxqt-build-tools" ,lxqt-build-tools))) + (home-page "https://lxqt.org/") (synopsis "Core utility library for all LXQt components") (description "liblxqt provides the basic libraries shared by the components of the LXQt desktop environment.") diff --git a/gnu/packages/patches/liblxqt-include.patch b/gnu/packages/patches/liblxqt-include.patch deleted file mode 100644 index 4e8cf04789..0000000000 --- a/gnu/packages/patches/liblxqt-include.patch +++ /dev/null @@ -1,14 +0,0 @@ -Patch to fix build with Qt 5.5, taken from upstream: - https://github.com/lxde/liblxqt/commit/7303ea207de0771d6f450a31ec4a1ce69202869b - -diff -u -r liblxqt-0.9.0.orig/lxqtnotification.h liblxqt-0.9.0/lxqtnotification.h ---- liblxqt-0.9.0.orig/lxqtnotification.h 2015-07-27 22:49:05.365166482 +0200 -+++ liblxqt-0.9.0/lxqtnotification.h 2015-07-27 22:49:36.897606619 +0200 -@@ -25,6 +25,7 @@ - #ifndef LXQTNOTIFICATION_H - #define LXQTNOTIFICATION_H - -+#include - #include - #include "lxqtglobals.h" - From b45688313b525a8c590136adb62624d109ee73c4 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 21 Oct 2018 23:38:29 +0200 Subject: [PATCH 46/58] gnu: python-mistune: Update to 0.8.4. * gnu/packages/python.scm (python-mistune): Update to 0.8.4. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 9c749227de..d189438dec 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6004,14 +6004,14 @@ (define-public python2-flake8-polyfill (define-public python-mistune (package (name "python-mistune") - (version "0.8.3") + (version "0.8.4") (source (origin (method url-fetch) (uri (pypi-uri "mistune" version)) (sha256 (base32 - "06b662p6kf46wh2jsabaqhaq4bz1srh2zxkrnx4yg96azlxw645w")))) + "0vkmsh0x480rni51lhyvigfdf06b9247z868pk3bal1wnnfl58sr")))) (build-system python-build-system) (native-inputs `(("python-nose" ,python-nose) From f232c875d2d591eac99e0168652ecbcb3d21a8ff Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 21 Oct 2018 23:53:16 +0200 Subject: [PATCH 47/58] gnu: python-lazy-object-proxy: Update to 1.3.1. * gnu/packages/python.scm (python-lazy-object-proxy): Update to 1.3.1. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index d189438dec..c39a53d8d9 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9578,13 +9578,13 @@ (define-public python2-cleo (define-public python-lazy-object-proxy (package (name "python-lazy-object-proxy") - (version "1.2.2") + (version "1.3.1") (source (origin (method url-fetch) (uri (pypi-uri "lazy-object-proxy" version)) (sha256 (base32 - "0s22aqqkdscyh8sjspyyax7qa1aiz8p4midrnyf39717fhfczm6x")))) + "0yha7q9bhw857fwaby785d63mffhngl9npwzlk9i0pwlkwvbx4gb")))) (build-system python-build-system) (home-page "https://github.com/ionelmc/python-lazy-object-proxy") (synopsis "Lazy object proxy for python") From 3ad0a35890ea3142e0ac16a8be6addd1693a10a1 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 12 Sep 2018 13:45:34 +0200 Subject: [PATCH 48/58] gnu: Add GN. * gnu/packages/build-tools.scm (gn): New public variable. --- gnu/packages/build-tools.scm | 58 ++++++++++++++++++++++++++++++++++++ 1 file changed, 58 insertions(+) diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm index 4fc2d5acf7..42de56f8c3 100644 --- a/gnu/packages/build-tools.scm +++ b/gnu/packages/build-tools.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2018 Fis Trivial ;;; Copyright © 2018 Tomáš Čech +;;; Copyright © 2018 Marius Bakke ;;; ;;; This file is part of GNU Guix. ;;; @@ -98,6 +99,63 @@ (define-public bear generate such a compilation database.") (license license:gpl3+))) +(define-public gn + (let ((commit "f73698ebb33e26a0bf120e2b55d12528fd1dbe7d") + (revision "1481")) ;as returned by `git describe`, used below + (package + (name "gn") + (version (git-version "0.0" revision commit)) + (home-page "https://gn.googlesource.com/gn") + (source (origin + (method git-fetch) + (uri (git-reference (url home-page) (commit commit))) + (sha256 + (base32 + "078ydwak4424bkqh3hd7q955zxp2c3qlw44lsb29i8jqap140f9d")) + (file-name (git-file-name name version)))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ;FIXME: How to run? + #:phases (modify-phases %standard-phases + (add-before 'configure 'set-build-environment + (lambda _ + (setenv "CC" "gcc") (setenv "CXX" "g++") + (setenv "AR" "ar") + #t)) + (replace 'configure + (lambda _ + (invoke "python" "build/gen.py" "--no-sysroot" + "--no-last-commit-position"))) + (add-after 'configure 'create-last-commit-position + (lambda _ + ;; Create "last_commit_position.h" to avoid a dependency + ;; on 'git' (and the checkout..). + (call-with-output-file "out/last_commit_position.h" + (lambda (port) + (format port + "#define LAST_COMMIT_POSITION \"~a (~a)\"\n" + ,revision ,(string-take commit 8)) + #t)))) + (replace 'build + (lambda _ + (invoke "ninja" "-C" "out" "gn" + "-j" (number->string (parallel-job-count))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (install-file "out/gn" (string-append out "/bin")) + #t)))))) + (native-inputs + `(("ninja" ,ninja) + ("python" ,python-2))) + (synopsis "Generate Ninja build files") + (description + "GN is a tool that collects information about a project from @file{.gn} +files and generates build instructions for the Ninja build system.") + ;; GN is distributed as BSD-3, but bundles some files from ICU using the + ;; X11 license. + (license (list license:bsd-3 license:x11))))) + (define-public meson (package (name "meson") From f38eedd518816707cd407879f2f862095960b9fc Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:12:37 +0200 Subject: [PATCH 49/58] gnu: samba: Update to 4.8.6. * gnu/packages/samba.scm (samba): Update to 4.8.6. --- gnu/packages/samba.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm index a6d6ee30cd..458ff50ae8 100644 --- a/gnu/packages/samba.scm +++ b/gnu/packages/samba.scm @@ -150,14 +150,14 @@ (define (install dir) (define-public samba (package (name "samba") - (version "4.8.5") + (version "4.8.6") (source (origin (method url-fetch) (uri (string-append "https://download.samba.org/pub/samba/stable/" "samba-" version ".tar.gz")) (sha256 (base32 - "0mailvhjsma19k6b6zjl02z9n2hbbyfybvicjfw2hh9d4sqyd3p5")))) + "15hawqdm37l6lp9k14c634315p77cllsx89bvbw9h38fg1hj3fbk")))) (build-system gnu-build-system) (arguments `(#:phases From 3743e117a6424f6463d8abfca4dd71ce576a918a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:15:02 +0200 Subject: [PATCH 50/58] gnu: libmd: Update to 1.0.1. * gnu/packages/crypto.scm (libmd): Update to 1.0.1. --- gnu/packages/crypto.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index 77b4dba6d4..29d9a3d6ab 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -94,7 +94,7 @@ (define-public libsodium (define-public libmd (package (name "libmd") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri @@ -105,7 +105,7 @@ (define-public libmd version ".tar.xz"))) (sha256 (base32 - "1iv45npzv0gncjgcpx5m081861zdqxw667ysghqb8721yrlyl6pj")))) + "0waclg2d5qin3r26gy5jvy4584ik60njc8pqbzwk0lzq3j9ynkp1")))) (build-system gnu-build-system) (synopsis "Message Digest functions from BSD systems") (description From 4350cacdf73f6e589a7d19b147f3707836e30210 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:19:16 +0200 Subject: [PATCH 51/58] gnu: xf86-input-libinput: Update to 0.28.1. * gnu/packages/xorg.scm (xf86-input-libinput): Update to 0.28.1. --- gnu/packages/xorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 4cf8eb2de4..dff50e9919 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -2448,7 +2448,7 @@ (define-public xf86-input-evdev (define-public xf86-input-libinput (package (name "xf86-input-libinput") - (version "0.28.0") + (version "0.28.1") (source (origin (method url-fetch) (uri (string-append @@ -2456,7 +2456,7 @@ (define-public xf86-input-libinput name "-" version ".tar.bz2")) (sha256 (base32 - "189h8vl0005yizwrs4d0sng6j8lwkd3xi1zwqg8qavn2bw34v691")))) + "12yr0yki94j2416bfhmkz5jpacffm27jkra89fl7h03c0y749nls")))) (build-system gnu-build-system) (arguments '(#:configure-flags From 90fb136ff72533d138ae0153bee1f88a8bf58115 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:21:08 +0200 Subject: [PATCH 52/58] gnu: xorg-server: Update to 1.20.2. * gnu/packages/xorg.scm (xorg-server): Update to 1.20.2. --- gnu/packages/xorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index dff50e9919..86b4470aa0 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -5065,7 +5065,7 @@ (define-public libxcb (define-public xorg-server (package (name "xorg-server") - (version "1.20.1") + (version "1.20.2") (source (origin (method url-fetch) @@ -5074,7 +5074,7 @@ (define-public xorg-server name "-" version ".tar.bz2")) (sha256 (base32 - "0679942x1ma2p30vlvqylpjc5v1ak1pgqysnqrj82nz7dzl9zjar")) + "1qnf7jdygdgbgjfm5mfr691dl8d56mpssa82mvhm8bzj92yggm8f")) (patches (list ;; See: From e810de3e68db1e892688dc21a8804df066ff218b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:23:15 +0200 Subject: [PATCH 53/58] gnu: python-m2crypto: python-typing is only needed for python2. * gnu/packages/python-crypto.scm (python-m2crypto)[propagated-inputs]: Remove. [properties]: New field. (python2-m2crypto)[propagated-inputs]: Add PYTHON2-TYPING. --- gnu/packages/python-crypto.scm | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index bda547417c..8bee14c695 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -859,7 +859,6 @@ (define-public python-m2crypto (base32 "1h16gpilrnlzc0iyj1mnd1iqh8wchzjsxjqw9n344glimg2s5zm0")))) (build-system python-build-system) (inputs `(("openssl" ,openssl))) - (propagated-inputs `(("python-typing" ,python-typing))) (home-page "https://gitlab.com/m2crypto/m2crypto") (synopsis "Python crypto and TLS toolkit") (description "@code{M2Crypto} is a complete Python wrapper for OpenSSL @@ -869,10 +868,15 @@ (define-public python-m2crypto AuthCookies for web session management; FTP/TLS client and server; S/MIME; M2Crypto can also be used to provide TLS for Twisted. Smartcards supported through the Engine interface.") + (properties `((python2-variant . ,(delay python2-m2crypto)))) (license license:expat))) (define-public python2-m2crypto - (package-with-python2 python-m2crypto)) + (let ((m2crypto (package-with-python2 + (strip-python2-variant python-m2crypto)))) + (package (inherit m2crypto) + (propagated-inputs + `(("python2-typing" ,python2-typing)))))) (define-public python-pylibscrypt (package From cb61baf0e72e0756c3386acb0d7745c507daa3ac Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:24:28 +0200 Subject: [PATCH 54/58] gnu: python-m2crypto: Update to 0.30.1. * gnu/packages/python-crypto.scm (python-m2crypto): Update to 0.30.1. --- gnu/packages/python-crypto.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 8bee14c695..f71b8a3467 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -850,13 +850,13 @@ (define-public python2-pycryptodome (define-public python-m2crypto (package (name "python-m2crypto") - (version "0.29.0") + (version "0.30.1") (source (origin (method url-fetch) (uri (pypi-uri "M2Crypto" version)) (sha256 - (base32 "1h16gpilrnlzc0iyj1mnd1iqh8wchzjsxjqw9n344glimg2s5zm0")))) + (base32 "1iizrpkn4c2n70nvcjqlmnk6fz3vddkrjmwavz1zlsnwv8f7bcm1")))) (build-system python-build-system) (inputs `(("openssl" ,openssl))) (home-page "https://gitlab.com/m2crypto/m2crypto") From 1b50df7d5b13921eb61bfd81787d4d5596064cc6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:31:56 +0200 Subject: [PATCH 55/58] gnu: python-markdown: Update home page. * gnu/packages/python.scm (python-markdown)[home-page]: Change to current. --- gnu/packages/python.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index c39a53d8d9..b95774e9f7 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6046,7 +6046,7 @@ (define-public python-markdown (native-inputs `(("python-nose" ,python-nose) ("python-pyyaml" ,python-pyyaml))) - (home-page "https://pythonhosted.org/Markdown/") + (home-page "https://python-markdown.github.io/") (synopsis "Python implementation of Markdown") (description "This package provides a Python implementation of John Gruber's From 9b9aaa57e3bf8e75305b557e79b79f90e4fb331c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:32:41 +0200 Subject: [PATCH 56/58] gnu: python-markdown: Update to 3.0.1. * gnu/packages/python.scm (python-markdown): Update to 3.0.1. [arguments]: Remove. --- gnu/packages/python.scm | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index b95774e9f7..7e2082e5f2 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6028,21 +6028,15 @@ (define-public python2-mistune (define-public python-markdown (package (name "python-markdown") - (version "2.6.11") + (version "3.0.1") (source (origin (method url-fetch) (uri (pypi-uri "Markdown" version)) (sha256 (base32 - "108g80ryzykh8bj0i7jfp71510wrcixdi771lf2asyghgyf8cmm8")))) + "0z6v8649sr434d5r5zmrhydka7v7f9yas4bwcgkcs0650jdhybnh")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda _ - (zero? (system* "python" "run-tests.py"))))))) (native-inputs `(("python-nose" ,python-nose) ("python-pyyaml" ,python-pyyaml))) From 47d7c10387f391b107acd612137f247be506c46a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:37:49 +0200 Subject: [PATCH 57/58] gnu: python-sure: Update to 1.4.11. * gnu/packages/python.scm (python-sure): Update to 1.4.11. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 7e2082e5f2..664f7720ff 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -11933,14 +11933,14 @@ (define-public python2-radon (define-public python-sure (package (name "python-sure") - (version "1.4.6") + (version "1.4.11") (source (origin (method url-fetch) (uri (pypi-uri "sure" version)) (sha256 (base32 - "1iyqsy2d6radi88g1qf0lziy5b39h5cpb3g5jiqyb4xi46ig3x1z")))) + "1and0drq8w9iplsic22n2h7hkpyq03a1mbqk4sgcdqhqzdqm539w")))) (build-system python-build-system) (propagated-inputs `(("python-mock" ,python-mock) From 63abd1e2a36d48e1f8f7057a4c844b9cf5733be7 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:53:38 +0200 Subject: [PATCH 58/58] gnu: python-pymongo: Update to 3.7.2. * gnu/packages/python.scm (python-pymongo): Update to 3.7.2. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 664f7720ff..dee7d9a06a 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10060,13 +10060,13 @@ (define-public python2-nltk (define-public python-pymongo (package (name "python-pymongo") - (version "3.3.0") + (version "3.7.2") (source (origin (method url-fetch) (uri (pypi-uri "pymongo" version)) (sha256 (base32 - "07mra6w86wjqy4lx5fvimidjhhfzd562gfjn8grsnbv2q8pk0i9x")))) + "0zis4707r9hdg5qgkhp3wss9camr9h56ixyfc8n9dxwlnnly4x4c")))) (build-system python-build-system) (propagated-inputs `(("python-certifi" ,python-certifi)))