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04/04: gnu: pigx-sars-cov2-ww: Remove dependency on pandoc-citeproc.
From: |
guix-commits |
Subject: |
04/04: gnu: pigx-sars-cov2-ww: Remove dependency on pandoc-citeproc. |
Date: |
Tue, 5 Oct 2021 13:12:23 -0400 (EDT) |
lbraun pushed a commit to branch wip-haskell
in repository guix.
commit 1b3dc9153de2f40f164e5ea6e1022e18ccbb6d57
Author: Lars-Dominik Braun <lars@6xq.net>
AuthorDate: Tue Oct 5 19:08:36 2021 +0200
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.
---
gnu/local.mk | 1 +
gnu/packages/bioinformatics.scm | 12 +++++++-
.../patches/pigx-sars-cov2-ww-no-citeproc.patch | 33 ++++++++++++++++++++++
3 files changed, 45 insertions(+), 1 deletion(-)
diff --git a/gnu/local.mk b/gnu/local.mk
index ac10356..7ea976c 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1589,6 +1589,7 @@ 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 a59c8ca..ef526e1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10782,8 +10782,18 @@ 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 0000000..3f34bca
--- /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']