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gnu: pigx-sars-cov2-ww: Update to 0.0.5.

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* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.5.
[source]: Remove patch.
[arguments]: Disable tests.
* gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
This commit is contained in:
Ricardo Wurmus 2022-03-29 13:49:50 +02:00
parent 847acc3206
commit 6d5964e804
No known key found for this signature in database
GPG key ID: 197A5888235FACAC
3 changed files with 4 additions and 38 deletions
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1
gnu/local.mk
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@ -1628,7 +1628,6 @@ dist_patch_DATA = \
%D%/packages/patches/pidgin-add-search-path.patch \
%D%/packages/patches/pigx-bsseq-no-citeproc.patch \
%D%/packages/patches/pigx-chipseq-no-citeproc.patch \
%D%/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch \
%D%/packages/patches/pigx-scrnaseq-no-citeproc.patch \
%D%/packages/patches/pinball-system-ltdl.patch \
%D%/packages/patches/pingus-boost-headers.patch \

8
gnu/packages/bioinformatics.scm
View file

@ -11192,7 +11192,7 @@ based methods.")
(define-public pigx-sars-cov2-ww
(package
(name "pigx-sars-cov2-ww")
(version "0.0.4")
(version "0.0.5")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_sarscov2_ww/"
@ -11200,11 +11200,11 @@ based methods.")
"/pigx_sars-cov2-ww-" version ".tar.gz"))
(sha256
(base32
"0axnmz4d8zgir888mc0cilcq4m3v41xmjmpp3w3444lciwnxydvs"))
(patches (search-patches "pigx-sars-cov2-ww-no-citeproc.patch"))))
"1fkr9gp09zl5n7kdqmy9lrnq28k2z97wg74wgkyfssfyxvmq9cr2"))))
(build-system gnu-build-system)
(arguments
`(#:phases
`(#:tests? #f ;requires huge kraken database
#:phases
(modify-phases %standard-phases
(add-before 'bootstrap 'autoreconf
(lambda _

33
gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch
View file

@ -1,33 +0,0 @@
diff -Naur pigx_sars-cov2-ww-0.0.3/configure.ac pigx_sars-cov2-ww-0.0.3.patched/configure.ac
--- pigx_sars-cov2-ww-0.0.3/configure.ac 2021-06-10 10:12:00.552889984 +0200
+++ pigx_sars-cov2-ww-0.0.3.patched/configure.ac 2021-10-05 14:52:32.318695129 +0200
@@ -50,7 +50,6 @@
find_or_override_prog([MULTIQC], [multiqc])
find_or_override_prog([WGET], [wget])
find_or_override_prog([PANDOC], [pandoc])
-find_or_override_prog([PANDOC_CITEPROC], [pandoc-citeproc])
AC_ARG_ENABLE([r-packages-check],
AS_HELP_STRING([--disable-r-packages-check], [Do not check any R packages.]),
diff -Naur pigx_sars-cov2-ww-0.0.3/Makefile.in pigx_sars-cov2-ww-0.0.3.patched/Makefile.in
--- pigx_sars-cov2-ww-0.0.3/Makefile.in 2021-08-05 16:33:59.164123383 +0200
+++ pigx_sars-cov2-ww-0.0.3.patched/Makefile.in 2021-10-05 14:52:41.272958547 +0200
@@ -402,7 +402,6 @@
PACKAGE_URL = @PACKAGE_URL@
PACKAGE_VERSION = @PACKAGE_VERSION@
PANDOC = @PANDOC@
-PANDOC_CITEPROC = @PANDOC_CITEPROC@
PATH_SEPARATOR = @PATH_SEPARATOR@
PRINSEQ = @PRINSEQ@
PYTHON = @PYTHON@
diff -Naur pigx_sars-cov2-ww-0.0.3/pigx-common/common/pigx-runner.in pigx_sars-cov2-ww-0.0.3.patched/pigx-common/common/pigx-runner.in
--- pigx_sars-cov2-ww-0.0.3/pigx-common/common/pigx-runner.in 2021-07-30 11:10:17.913115902 +0200
+++ pigx_sars-cov2-ww-0.0.3.patched/pigx-common/common/pigx-runner.in 2021-10-05 14:52:23.602438714 +0200
@@ -379,7 +379,6 @@
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']