03/03: gnu: pigx-scrnaseq: Remove dependency on pandoc-citeproc.

[guix-commits]

lbraun pushed a commit to branch wip-haskell
in repository guix.

commit d8ce90ab44d04fa95b32fd2803f3e1997aec70f8
Author: Lars-Dominik Braun <lars@6xq.net>
AuthorDate: Wed Oct 6 14:11:15 2021 +0200

    gnu: pigx-scrnaseq: Remove dependency on pandoc-citeproc.
    
    * gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Add patch.
    * gnu/local.mk: Register it.
    * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[source]: Use it.
    [native-inputs]: Add automake/autoconf.
---
 gnu/local.mk                                       |  1 +
 gnu/packages/bioinformatics.scm                    | 12 +++++++-
 .../patches/pigx-scrnaseq-no-citeproc.patch        | 33 ++++++++++++++++++++++
 3 files changed, 45 insertions(+), 1 deletion(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 5bd1b82..ea9afb9 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1592,6 +1592,7 @@ dist_patch_DATA =                                         
\
   %D%/packages/patches/pigx-chipseq-no-citeproc.patch          \
   %D%/packages/patches/pigx-rnaseq-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              \
   %D%/packages/patches/pingus-sdl-libs-config.patch            \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index caba3c1..1b3b096 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10731,8 +10731,18 @@ methylation and segmentation.")
                                   "/pigx_scrnaseq-" version ".tar.gz"))
               (sha256
                (base32
-                "1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx"))))
+                "1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx"))
+              (patches (search-patches "pigx-scrnaseq-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
      `(("coreutils" ,coreutils)
        ("perl" ,perl)
diff --git a/gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch 
b/gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch
new file mode 100644
index 0000000..4cce33f
--- /dev/null
+++ b/gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch
@@ -0,0 +1,33 @@
+diff -Naur pigx_scrnaseq-1.1.7/configure.ac 
pigx_scrnaseq-1.1.7.patched/configure.ac
+--- pigx_scrnaseq-1.1.7/configure.ac   2020-03-17 14:37:46.000000000 +0100
++++ pigx_scrnaseq-1.1.7.patched/configure.ac   2021-10-06 13:55:49.779271317 
+0200
+@@ -43,7 +43,6 @@
+ 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([STAR],            [STAR])
+ find_or_override_prog([SAMTOOLS],        [samtools])
+diff -Naur pigx_scrnaseq-1.1.7/Makefile.in 
pigx_scrnaseq-1.1.7.patched/Makefile.in
+--- pigx_scrnaseq-1.1.7/Makefile.in    2020-11-30 16:55:48.000000000 +0100
++++ pigx_scrnaseq-1.1.7.patched/Makefile.in    2021-10-06 13:55:52.224340194 
+0200
+@@ -395,7 +395,6 @@
+ PACKAGE_URL = @PACKAGE_URL@
+ PACKAGE_VERSION = @PACKAGE_VERSION@
+ PANDOC = @PANDOC@
+-PANDOC_CITEPROC = @PANDOC_CITEPROC@
+ PATH_SEPARATOR = @PATH_SEPARATOR@
+ PERL = @PERL@
+ PYTHON = @PYTHON@
+diff -Naur pigx_scrnaseq-1.1.7/pigx-scrnaseq.in 
pigx_scrnaseq-1.1.7.patched/pigx-scrnaseq.in
+--- pigx_scrnaseq-1.1.7/pigx-scrnaseq.in       2020-11-30 16:08:55.000000000 
+0100
++++ pigx_scrnaseq-1.1.7.patched/pigx-scrnaseq.in       2021-10-06 
13:55:47.889218079 +0200
+@@ -274,7 +274,6 @@
+     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']