23/24: gnu: pigx-rnaseq: Remove dependency on pandoc-citeproc.

[guix-commits]

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

commit 61433870ea2cff83156d9989608d6a0e346b352b
Author: Lars-Dominik Braun <lars@6xq.net>
AuthorDate: Wed Oct 6 14:10:18 2021 +0200

    gnu: pigx-rnaseq: Remove dependency on pandoc-citeproc.
    
    * gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Add patch.
    * gnu/local.mk: Register it.
    * gnu/packages/bioinformatics.scm (pigx-rnaseq)[source]: Use it.
    [native-inputs]: Add automake/autoconf.
---
 gnu/local.mk                                       |  1 +
 gnu/packages/bioinformatics.scm                    | 10 +++++--
 gnu/packages/patches/pigx-rnaseq-no-citeproc.patch | 33 ++++++++++++++++++++++
 3 files changed, 42 insertions(+), 2 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 48ba7cf..d4e042d 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1601,6 +1601,7 @@ 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-rnaseq-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              \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 150bbc3..f5de168 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10489,7 +10489,8 @@ once.  This package provides tools to perform Drop-seq 
analyses.")
                                   "/pigx_rnaseq-" version ".tar.gz"))
               (sha256
                (base32
-                "1ja3bda1appxrzbfy7wp7khy30mm7lic8xbq3gkbpc5bld3as9cm"))))
+                "1ja3bda1appxrzbfy7wp7khy30mm7lic8xbq3gkbpc5bld3as9cm"))
+              (patches (search-patches "pigx-rnaseq-no-citeproc.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-tests? #f             ; not supported
@@ -10502,6 +10503,9 @@ once.  This package provides tools to perform Drop-seq 
analyses.")
              (substitute* "Makefile.in"
                (("^  tests/test_multiqc/test.sh") "")
                (("^  test.sh") ""))))
+         (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)
@@ -10545,7 +10549,9 @@ once.  This package provides tools to perform Drop-seq 
analyses.")
        ("python-deeptools" ,python-deeptools)
        ("python-pyyaml" ,python-pyyaml)))
     (native-inputs
-     `(("tzdata" ,tzdata)))
+     `(("tzdata" ,tzdata)
+       ("automake" ,automake)
+       ("autoconf" ,autoconf)))
     (home-page "https://bioinformatics.mdc-berlin.de/pigx/";)
     (synopsis "Analysis pipeline for RNA sequencing experiments")
     (description "PiGX RNAseq is an analysis pipeline for preprocessing and
diff --git a/gnu/packages/patches/pigx-rnaseq-no-citeproc.patch 
b/gnu/packages/patches/pigx-rnaseq-no-citeproc.patch
new file mode 100644
index 0000000..366ae38
--- /dev/null
+++ b/gnu/packages/patches/pigx-rnaseq-no-citeproc.patch
@@ -0,0 +1,33 @@
+diff -Naur pigx_rnaseq-0.0.19/configure.ac 
pigx_rnaseq-0.0.19.patched/configure.ac
+--- pigx_rnaseq-0.0.19/configure.ac    2021-07-23 14:01:00.304391428 +0200
++++ pigx_rnaseq-0.0.19.patched/configure.ac    2021-10-06 13:51:29.512960106 
+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([STAR],            [STAR])
+ find_or_override_prog([HISAT2],          [hisat2])
+ find_or_override_prog([HISAT2_BUILD],    [hisat2-build])
+diff -Naur pigx_rnaseq-0.0.19/Makefile.in 
pigx_rnaseq-0.0.19.patched/Makefile.in
+--- pigx_rnaseq-0.0.19/Makefile.in     2021-08-13 13:40:10.402922844 +0200
++++ pigx_rnaseq-0.0.19.patched/Makefile.in     2021-10-06 13:51:04.052247524 
+0200
+@@ -410,7 +410,6 @@
+ 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_rnaseq-0.0.19/pigx-common/common/pigx-runner.in 
pigx_rnaseq-0.0.19.patched/pigx-common/common/pigx-runner.in
+--- pigx_rnaseq-0.0.19/pigx-common/common/pigx-runner.in       2021-08-13 
13:27:50.494352532 +0200
++++ pigx_rnaseq-0.0.19.patched/pigx-common/common/pigx-runner.in       
2021-10-06 13:51:38.798220108 +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']