gnu: pigx-chipseq: Remove dependency on pandoc-citeproc.

* gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-chipseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.

3 files changed, 46 insertions, 4 deletions

diff --git a/gnu/local.mk b/gnu/local.mk
index 9c8a777d19..71f1a25f83 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-chipseq-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 ed4470e313..150bbc361f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10567,10 +10567,16 @@ expression report comparing samples in an easily configurable manner.")
                                   "/pigx_chipseq-" version ".tar.gz"))
               (sha256
                (base32
-                "0c6npx35sszycf059w1x1k4k9hq1qqxny0i4p57q1188czr4561h"))))
+                "0c6npx35sszycf059w1x1k4k9hq1qqxny0i4p57q1188czr4561h"))
+              (patches (search-patches "pigx-chipseq-no-citeproc.patch"))))
     (build-system gnu-build-system)
-    ;; parts of the tests rely on access to the network
-    (arguments '(#:tests? #f))
+    (arguments
+     `(#:tests? #f ; parts of the tests rely on access to the network
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'bootstrap 'autoreconf
+           (lambda _
+             (invoke "autoreconf" "-vif"))))))
     (inputs
      `(("grep" ,grep)
        ("coreutils" ,coreutils)
@@ -10621,7 +10627,9 @@ expression report comparing samples in an easily configurable manner.")
        ("bedtools" ,bedtools)
        ("kentutils" ,kentutils)))
     (native-inputs
-     `(("python-pytest" ,python-pytest)))
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("python-pytest" ,python-pytest)))
     (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
     (synopsis "Analysis pipeline for ChIP sequencing experiments")
     (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak
diff --git a/gnu/packages/patches/pigx-chipseq-no-citeproc.patch b/gnu/packages/patches/pigx-chipseq-no-citeproc.patch
new file mode 100644
index 0000000000..b01820f110
--- /dev/null
+++ b/gnu/packages/patches/pigx-chipseq-no-citeproc.patch
@@ -0,0 +1,33 @@
+diff -Naur pigx_chipseq-0.0.53/configure.ac pigx_chipseq-0.0.53.patched/configure.ac
+--- pigx_chipseq-0.0.53/configure.ac	2021-09-28 11:14:12.000000000 +0200
++++ pigx_chipseq-0.0.53.patched/configure.ac	2021-10-07 14:48:53.034054327 +0200
+@@ -52,7 +52,6 @@
+ find_or_override_prog([MACS2],           [macs2])
+ 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([BOWTIE2],         [bowtie2])
+ find_or_override_prog([BOWTIE2_BUILD],   [bowtie2-build])
+diff -Naur pigx_chipseq-0.0.53/Makefile.in pigx_chipseq-0.0.53.patched/Makefile.in
+--- pigx_chipseq-0.0.53/Makefile.in	2021-09-28 11:55:05.000000000 +0200
++++ pigx_chipseq-0.0.53.patched/Makefile.in	2021-10-07 14:48:37.195577143 +0200
+@@ -407,7 +407,6 @@
+ 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_chipseq-0.0.53/pigx-common/common/pigx-runner.in pigx_chipseq-0.0.53.patched/pigx-common/common/pigx-runner.in
+--- pigx_chipseq-0.0.53/pigx-common/common/pigx-runner.in	2021-09-27 18:16:42.000000000 +0200
++++ pigx_chipseq-0.0.53.patched/pigx-common/common/pigx-runner.in	2021-10-07 14:48:44.200788218 +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']