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| author | Lars-Dominik Braun <lars@6xq.net> | 2021-10-05 19:08:36 +0200 |
|---|---|---|
| committer | Lars-Dominik Braun <lars@6xq.net> | 2021-10-08 09:13:54 +0200 |
| commit | e51a3f4a727d8bd74ccef6322a422c7e8a421394 (patch) | |
| tree | 65e347056d1f9585ec577d9105cbef3525f44e32 /gnu/packages | |
| parent | fb1ffc53ba6177e28aa296ae2e9c2e812f92e28e (diff) | |
| download | guix-e51a3f4a727d8bd74ccef6322a422c7e8a421394.tar.gz guix-e51a3f4a727d8bd74ccef6322a422c7e8a421394.zip | |
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.
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 12 | ||||
| -rw-r--r-- | gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch | 33 |
2 files changed, 44 insertions, 1 deletions
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'] |