gnu: pigx-sars-cov2-ww: Remove dependency on pandoc-citeproc.

* gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww)[source]: Use it.
[native-inputs]: Add automake/autoconf.

3 files changed, 45 insertions, 1 deletions

diff --git a/gnu/local.mk b/gnu/local.mk
index c34da97634..9c8a777d19 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-sars-cov2-ww-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 63e91438cb..ed4470e313 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10783,8 +10783,18 @@ based methods.")
                                   "/pigx_sars-cov2-ww-" version ".tar.gz"))
               (sha256
                (base32
-                "1hhdbwsnl0d37lrmisw5hr630xr8s41qvxflm05anh11rj8n22yw"))))
+                "1hhdbwsnl0d37lrmisw5hr630xr8s41qvxflm05anh11rj8n22yw"))
+              (patches (search-patches "pigx-sars-cov2-ww-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
      `(("bash-minimal" ,bash-minimal)
        ("bwa" ,bwa)
diff --git a/gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch b/gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch
new file mode 100644
index 0000000000..3f34bca6b2
--- /dev/null
+++ b/gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch
@@ -0,0 +1,33 @@
+diff -Naur pigx_sars-cov2-ww-0.0.3/configure.ac pigx_sars-cov2-ww-0.0.3.patched/configure.ac
+--- pigx_sars-cov2-ww-0.0.3/configure.ac	2021-06-10 10:12:00.552889984 +0200
++++ pigx_sars-cov2-ww-0.0.3.patched/configure.ac	2021-10-05 14:52:32.318695129 +0200
+@@ -50,7 +50,6 @@
+ find_or_override_prog([MULTIQC],         [multiqc])
+ find_or_override_prog([WGET],            [wget])
+ find_or_override_prog([PANDOC],          [pandoc])
+-find_or_override_prog([PANDOC_CITEPROC], [pandoc-citeproc])
+ 
+ AC_ARG_ENABLE([r-packages-check],
+   AS_HELP_STRING([--disable-r-packages-check], [Do not check any R packages.]),
+diff -Naur pigx_sars-cov2-ww-0.0.3/Makefile.in pigx_sars-cov2-ww-0.0.3.patched/Makefile.in
+--- pigx_sars-cov2-ww-0.0.3/Makefile.in	2021-08-05 16:33:59.164123383 +0200
++++ pigx_sars-cov2-ww-0.0.3.patched/Makefile.in	2021-10-05 14:52:41.272958547 +0200
+@@ -402,7 +402,6 @@
+ PACKAGE_URL = @PACKAGE_URL@
+ PACKAGE_VERSION = @PACKAGE_VERSION@
+ PANDOC = @PANDOC@
+-PANDOC_CITEPROC = @PANDOC_CITEPROC@
+ PATH_SEPARATOR = @PATH_SEPARATOR@
+ PRINSEQ = @PRINSEQ@
+ PYTHON = @PYTHON@
+diff -Naur pigx_sars-cov2-ww-0.0.3/pigx-common/common/pigx-runner.in pigx_sars-cov2-ww-0.0.3.patched/pigx-common/common/pigx-runner.in
+--- pigx_sars-cov2-ww-0.0.3/pigx-common/common/pigx-runner.in	2021-07-30 11:10:17.913115902 +0200
++++ pigx_sars-cov2-ww-0.0.3.patched/pigx-common/common/pigx-runner.in	2021-10-05 14:52:23.602438714 +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']