summaryrefslogtreecommitdiff
path: root/gnu
diff options
context:
space:
mode:
authorLars-Dominik Braun <lars@6xq.net>2021-10-05 19:08:36 +0200
committerLars-Dominik Braun <lars@6xq.net>2021-10-08 09:13:54 +0200
commite51a3f4a727d8bd74ccef6322a422c7e8a421394 (patch)
tree65e347056d1f9585ec577d9105cbef3525f44e32 /gnu
parentfb1ffc53ba6177e28aa296ae2e9c2e812f92e28e (diff)
gnu: pigx-sars-cov2-ww: Remove dependency on pandoc-citeproc.
* gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww)[source]: Use it. [native-inputs]: Add automake/autoconf.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/local.mk1
-rw-r--r--gnu/packages/bioinformatics.scm12
-rw-r--r--gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch33
3 files changed, 45 insertions, 1 deletions
diff --git a/gnu/local.mk b/gnu/local.mk
index c34da97634..9c8a777d19 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1600,6 +1600,7 @@ dist_patch_DATA = \
%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/pigx-sars-cov2-ww-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 \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 63e91438cb..ed4470e313 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10783,8 +10783,18 @@ based methods.")
"/pigx_sars-cov2-ww-" version ".tar.gz"))
(sha256
(base32
- "1hhdbwsnl0d37lrmisw5hr630xr8s41qvxflm05anh11rj8n22yw"))))
+ "1hhdbwsnl0d37lrmisw5hr630xr8s41qvxflm05anh11rj8n22yw"))
+ (patches (search-patches "pigx-sars-cov2-ww-no-citeproc.patch"))))
(build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'bootstrap 'autoreconf
+ (lambda _
+ (invoke "autoreconf" "-vif"))))))
+ (native-inputs
+ `(("automake" ,automake)
+ ("autoconf" ,autoconf)))
(inputs
`(("bash-minimal" ,bash-minimal)
("bwa" ,bwa)
diff --git a/gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch b/gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch
new file mode 100644
index 0000000000..3f34bca6b2
--- /dev/null
+++ b/gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch
@@ -0,0 +1,33 @@
+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']