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Merge branch 'master' into core-updates

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Marius Bakke 2018-10-22 23:07:16 +02:00
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2
gnu/build/install.scm
View file

@ -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")

4
gnu/local.mk
View file

@ -635,7 +635,6 @@ 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 \
@ -644,7 +643,6 @@ 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 \
@ -890,7 +888,6 @@ 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 \
@ -1180,7 +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 \

26
gnu/packages/bioconductor.scm
View file

@ -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)))

658
gnu/packages/bioinformatics.scm
View file

@ -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)
@ -1383,7 +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
@ -1450,13 +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)
@ -1474,40 +1474,38 @@ (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")
(version "0.7.3")
(name "python-bx-python")
(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))
;; Tests fail because test data are not included
(arguments '(#:tests? #f))
(propagated-inputs
`(("python-numpy" ,python-numpy)
("python-six" ,python-six)))
(inputs
`(("python-numpy" ,python2-numpy)
("zlib" ,zlib)))
`(("zlib" ,zlib)))
(native-inputs
`(("python-nose" ,python2-nose)))
(home-page "http://bitbucket.org/james_taylor/bx-python/")
`(("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
"bx-python provides tools for manipulating biological data, particularly
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")
@ -1597,19 +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")
@ -1896,31 +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
@ -1934,22 +1919,46 @@ (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")
(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)))
@ -2044,15 +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")
@ -2082,14 +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")
@ -2101,7 +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
@ -2110,7 +2119,7 @@ (define-public deeptools
(file-name (git-file-name name version))
(sha256
(base32
"06fdpp6cg3xiwryxjhixvfysl4z0ps1crjgia587qa9ikqpsa7fd"))))
"1vggnf52g6q2vifdl4cyi7s2fnfqq0ky2zrkj5zv2qfzsc3p3siw"))))
(build-system python-build-system)
(arguments
`(#:phases
@ -2146,42 +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
@ -2195,14 +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
@ -2230,13 +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
@ -2264,106 +2274,102 @@ (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
(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)
@ -2379,6 +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")
@ -2474,17 +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
@ -2492,17 +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")
@ -2535,31 +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))))))
@ -2606,38 +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
@ -2646,7 +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
@ -3741,75 +3743,48 @@ (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
@ -5601,25 +5576,38 @@ (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/")
@ -5745,6 +5733,51 @@ (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
@ -5776,16 +5809,7 @@ (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

58
gnu/packages/build-tools.scm
View file

@ -4,6 +4,7 @@
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
;;; Copyright © 2018 Tomáš Čech <sleep_walker@gnu.org>
;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
;;;
;;; 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")

4
gnu/packages/crypto.scm
View file

@ -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

4
gnu/packages/dns.scm
View file

@ -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

8
gnu/packages/education.scm
View file

@ -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")

49
gnu/packages/emacs.scm
View file

@ -6,7 +6,7 @@
;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2017, 2018 Chris Marusich <cmmarusich@gmail.com>
;;; Copyright © 2015, 2016 Christopher Allan Webber <cwebber@dustycloud.org>
;;; Copyright © 2015, 2016, 2018 Christopher Lemmer Webber <cwebber@dustycloud.org>
;;; Copyright © 2016 Adriano Peluso <catonano@gmail.com>
;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 David Thompson <davet@gnu.org>
@ -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")
@ -12386,3 +12413,23 @@ (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+))))

6
gnu/packages/gnome.scm
View file

@ -4098,15 +4098,15 @@ (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

46
gnu/packages/linux.scm
View file

@ -30,6 +30,7 @@
;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
;;; Copyright © 2018 Brendan Tildesley <brendan.tildesley@openmailbox.org>
;;; Copyright © 2018 Manuel Graf <graf@init.at>
;;; Copyright © 2018 Pierre Langlois <pierre.langlois@gmx.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -399,8 +400,8 @@ (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
@ -430,8 +431,8 @@ (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
@ -440,14 +441,14 @@ (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))
(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))
@ -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

72
gnu/packages/lxqt.scm
View file

@ -5,6 +5,7 @@
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Meiyo Peng <meiyo.peng@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -31,30 +32,40 @@ (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
(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.")
@ -63,29 +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.")

4
gnu/packages/mpd.scm
View file

@ -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)

121
gnu/packages/patches/crossmap-allow-system-pysam.patch
View file

@ -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

56
gnu/packages/patches/delly-use-system-libraries.patch
View file

@ -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)

14
gnu/packages/patches/liblxqt-include.patch
View file

@ -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 <QObject>
#include <QStringList>
#include "lxqtglobals.h"

24
gnu/packages/patches/tophat-build-with-later-seqan.patch
View file

@ -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<uint32_t, IntronMotifs> MotifMap;
MotifMap ims;
-
- seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
- seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
-
+
+ typedef seqan::ModifiedString<
+ seqan::ModifiedString<seqan::DnaString const, seqan::ModView<seqan::FunctorComplement<seqan::Dna> > >,
+ 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");

12
gnu/packages/python-crypto.scm
View file

@ -850,16 +850,15 @@ (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)))
(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

54
gnu/packages/python.scm
View file

@ -55,6 +55,7 @@
;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
;;; Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2018 Luther Thompson <lutheroto@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -5904,14 +5905,14 @@ (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)
@ -5928,25 +5929,19 @@ (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)))
(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
@ -9462,13 +9457,13 @@ (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")
@ -9950,13 +9945,13 @@ (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)))
@ -11849,14 +11844,14 @@ (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)
@ -14429,3 +14424,28 @@ (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+)))

4
gnu/packages/samba.scm
View file

@ -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

4
gnu/packages/ssh.scm
View file

@ -134,14 +134,14 @@ (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)

189
gnu/packages/tex.scm
View file

@ -2288,6 +2288,44 @@ (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")
@ -4751,3 +4789,154 @@ (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+)))
(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)))
(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+)))
(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+)))

4
gnu/packages/video.scm
View file

@ -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, <xlocale.h> no longer is.

8
gnu/packages/xorg.scm
View file

@ -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
@ -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: