From fb1ffc53ba6177e28aa296ae2e9c2e812f92e28e Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <lars@6xq.net>
Date: Tue, 5 Oct 2021 15:42:38 +0200
Subject: gnu: pigx-bsseq: Remove dependency on pandoc-citeproc.

* gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-bsseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
---
 gnu/local.mk                                      |  1 +
 gnu/packages/bioinformatics.scm                   | 10 +++++--
 gnu/packages/patches/pigx-bsseq-no-citeproc.patch | 33 +++++++++++++++++++++++
 3 files changed, 42 insertions(+), 2 deletions(-)
 create mode 100644 gnu/packages/patches/pigx-bsseq-no-citeproc.patch

(limited to 'gnu')

diff --git a/gnu/local.mk b/gnu/local.mk
index 43bb7208ba..c34da97634 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1599,6 +1599,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/picard-fix-id3-rename-test.patch		\
   %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/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 932073ef5a..63e91438cb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10644,7 +10644,8 @@ in an easily configurable manner.")
                                   "/pigx_bsseq-" version ".tar.gz"))
               (sha256
                (base32
-                "05al5dacfp1vf1x3cq20jhd6w4xj5vaxslzaka6yrpg0av8sh3k3"))))
+                "05al5dacfp1vf1x3cq20jhd6w4xj5vaxslzaka6yrpg0av8sh3k3"))
+              (patches (search-patches "pigx-bsseq-no-citeproc.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(;; TODO: tests currently require 12+GB of RAM.  See
@@ -10652,6 +10653,9 @@ in an easily configurable manner.")
        #:tests? #f
        #:phases
        (modify-phases %standard-phases
+         (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)
@@ -10660,7 +10664,9 @@ in an easily configurable manner.")
                      (string-append (assoc-ref inputs "tzdata")
                                     "/share/zoneinfo")))))))
     (native-inputs
-     `(("tzdata" ,tzdata)))
+     `(("tzdata" ,tzdata)
+       ("automake" ,automake)
+       ("autoconf" ,autoconf)))
     (inputs
      `(("coreutils" ,coreutils)
        ("sed" ,sed)
diff --git a/gnu/packages/patches/pigx-bsseq-no-citeproc.patch b/gnu/packages/patches/pigx-bsseq-no-citeproc.patch
new file mode 100644
index 0000000000..882e660fe4
--- /dev/null
+++ b/gnu/packages/patches/pigx-bsseq-no-citeproc.patch
@@ -0,0 +1,33 @@
+diff -Naur pigx_bsseq-0.1.5/configure.ac pigx_bsseq-0.1.5.patched/configure.ac
+--- pigx_bsseq-0.1.5/configure.ac	2021-06-08 15:28:08.000000000 +0200
++++ pigx_bsseq-0.1.5.patched/configure.ac	2021-10-05 14:43:56.806529137 +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([FASTQC],          [fastqc])
+ find_or_override_prog([MULTIQC],         [multiqc])
+ find_or_override_prog([TRIMGALORE],      [trim_galore])
+diff -Naur pigx_bsseq-0.1.5/Makefile.in pigx_bsseq-0.1.5.patched/Makefile.in
+--- pigx_bsseq-0.1.5/Makefile.in	2021-06-08 16:17:03.000000000 +0200
++++ pigx_bsseq-0.1.5.patched/Makefile.in	2021-10-05 14:43:34.635876855 +0200
+@@ -408,7 +408,6 @@
+ 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_bsseq-0.1.5/pigx-common/common/pigx-runner.in pigx_bsseq-0.1.5.patched/pigx-common/common/pigx-runner.in
+--- pigx_bsseq-0.1.5/pigx-common/common/pigx-runner.in	2021-06-08 10:14:29.000000000 +0200
++++ pigx_bsseq-0.1.5.patched/pigx-common/common/pigx-runner.in	2021-10-05 14:43:44.296161069 +0200
+@@ -375,7 +375,6 @@
+     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']
-- 
cgit v1.2.3