01/03: gnu: pigx-chipseq: Remove dependency on pandoc-citeproc.

[guix-commits]

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

commit a828fefd53026ed78ae982bfe6387fe876bef325
Author: Lars-Dominik Braun <lars@6xq.net>
AuthorDate: Wed Oct 6 14:08:53 2021 +0200

    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.
---
 gnu/local.mk                                       |  1 +
 gnu/packages/bioinformatics.scm                    | 16 ++++++++---
 .../patches/pigx-chipseq-no-citeproc.patch         | 33 ++++++++++++++++++++++
 3 files changed, 46 insertions(+), 4 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 7ea976c..6bf3758 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-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 ef526e1..497b9fa 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
-                "097cvc8kr3r1nq0sgjpirzmixwjl074qp4qq3sx4ngfqi06af6r9"))))
+                "097cvc8kr3r1nq0sgjpirzmixwjl074qp4qq3sx4ngfqi06af6r9"))
+              (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)
@@ -10620,7 +10626,9 @@ 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 0000000..dc936a2
--- /dev/null
+++ b/gnu/packages/patches/pigx-chipseq-no-citeproc.patch
@@ -0,0 +1,33 @@
+diff -Naur pigx_chipseq-0.0.52/configure.ac 
pigx_chipseq-0.0.52.patched/configure.ac
+--- pigx_chipseq-0.0.52/configure.ac   2020-11-24 12:10:17.000000000 +0100
++++ pigx_chipseq-0.0.52.patched/configure.ac   2021-10-06 13:46:33.098556617 
+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-0.0.52/Makefile.in 
pigx_chipseq-0.0.52.patched/Makefile.in
+--- pigx_chipseq-0.0.52/Makefile.in    2021-05-12 18:06:02.000000000 +0200
++++ pigx_chipseq-0.0.52.patched/Makefile.in    2021-10-06 13:46:24.402309894 
+0200
+@@ -406,7 +406,6 @@
+ 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-0.0.52/pigx-chipseq.in 
pigx_chipseq-0.0.52.patched/pigx-chipseq.in
+--- pigx_chipseq-0.0.52/pigx-chipseq.in        2020-11-24 12:10:42.000000000 
+0100
++++ pigx_chipseq-0.0.52.patched/pigx-chipseq.in        2021-10-06 
13:46:41.977808549 +0200
+@@ -253,7 +253,6 @@
+     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['R_LIBS_USER'] = "/dev/null"