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gnu: pigx-bsseq: Remove dependency on pandoc-citeproc.

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* gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-bsseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
This commit is contained in:
Lars-Dominik Braun 2021-10-05 15:42:38 +02:00
parent ff5fea3dfe
commit fb1ffc53ba
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GPG key ID: F663943E08D8092A
3 changed files with 42 additions and 2 deletions
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1
gnu/local.mk
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@ -1599,6 +1599,7 @@ dist_patch_DATA = \
%D%/packages/patches/picard-fix-id3-rename-test.patch \
%D%/packages/patches/picprog-non-intel-support.patch \
%D%/packages/patches/pidgin-add-search-path.patch \
%D%/packages/patches/pigx-bsseq-no-citeproc.patch \
%D%/packages/patches/pinball-system-ltdl.patch \
%D%/packages/patches/pingus-boost-headers.patch \
%D%/packages/patches/pingus-sdl-libs-config.patch \

10
gnu/packages/bioinformatics.scm
View file

@ -10644,7 +10644,8 @@ (define-public pigx-bsseq
"/pigx_bsseq-" version ".tar.gz"))
(sha256
(base32
"05al5dacfp1vf1x3cq20jhd6w4xj5vaxslzaka6yrpg0av8sh3k3"))))
"05al5dacfp1vf1x3cq20jhd6w4xj5vaxslzaka6yrpg0av8sh3k3"))
(patches (search-patches "pigx-bsseq-no-citeproc.patch"))))
(build-system gnu-build-system)
(arguments
`(;; TODO: tests currently require 12+GB of RAM. See
@ -10652,6 +10653,9 @@ (define-public pigx-bsseq
#:tests? #f
#:phases
(modify-phases %standard-phases
(add-before 'bootstrap 'autoreconf
(lambda _
(invoke "autoreconf" "-vif")))
(add-before 'check 'set-timezone
;; The readr package is picky about timezones.
(lambda* (#:key inputs #:allow-other-keys)
@ -10660,7 +10664,9 @@ (define-public pigx-bsseq
(string-append (assoc-ref inputs "tzdata")
"/share/zoneinfo")))))))
(native-inputs
`(("tzdata" ,tzdata)))
`(("tzdata" ,tzdata)
("automake" ,automake)
("autoconf" ,autoconf)))
(inputs
`(("coreutils" ,coreutils)
("sed" ,sed)

33
gnu/packages/patches/pigx-bsseq-no-citeproc.patch Normal file
View file

@ -0,0 +1,33 @@
diff -Naur pigx_bsseq-0.1.5/configure.ac pigx_bsseq-0.1.5.patched/configure.ac
--- pigx_bsseq-0.1.5/configure.ac 2021-06-08 15:28:08.000000000 +0200
+++ pigx_bsseq-0.1.5.patched/configure.ac 2021-10-05 14:43:56.806529137 +0200
@@ -38,7 +38,6 @@
find_or_override_prog([GNUBASH], [bash])
find_or_override_prog([SNAKEMAKE], [snakemake])
find_or_override_prog([PANDOC], [pandoc])
-find_or_override_prog([PANDOC_CITEPROC], [pandoc-citeproc])
find_or_override_prog([FASTQC], [fastqc])
find_or_override_prog([MULTIQC], [multiqc])
find_or_override_prog([TRIMGALORE], [trim_galore])
diff -Naur pigx_bsseq-0.1.5/Makefile.in pigx_bsseq-0.1.5.patched/Makefile.in
--- pigx_bsseq-0.1.5/Makefile.in 2021-06-08 16:17:03.000000000 +0200
+++ pigx_bsseq-0.1.5.patched/Makefile.in 2021-10-05 14:43:34.635876855 +0200
@@ -408,7 +408,6 @@
PACKAGE_URL = @PACKAGE_URL@
PACKAGE_VERSION = @PACKAGE_VERSION@
PANDOC = @PANDOC@
-PANDOC_CITEPROC = @PANDOC_CITEPROC@
PATH_SEPARATOR = @PATH_SEPARATOR@
PYTHON = @PYTHON@
PYTHONPATH = @PYTHONPATH@
diff -Naur pigx_bsseq-0.1.5/pigx-common/common/pigx-runner.in pigx_bsseq-0.1.5.patched/pigx-common/common/pigx-runner.in
--- pigx_bsseq-0.1.5/pigx-common/common/pigx-runner.in 2021-06-08 10:14:29.000000000 +0200
+++ pigx_bsseq-0.1.5.patched/pigx-common/common/pigx-runner.in 2021-10-05 14:43:44.296161069 +0200
@@ -375,7 +375,6 @@
if path.exists(bin): shutil.rmtree(bin)
os.makedirs(bin, exist_ok=True)
os.symlink('@PANDOC@', path.join(bin, "pandoc"))
- os.symlink('@PANDOC_CITEPROC@', path.join(bin, "pandoc-citeproc"))
os.symlink('@RSCRIPT@', path.join(bin, "Rscript"))
os.environ['PATH'] = path.abspath(bin) + ":" + os.environ['PATH']
os.environ['PIGX_PATH'] = path.abspath(bin) + ":" + os.environ['PATH']