diff options
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 10 | ||||
| -rw-r--r-- | gnu/packages/patches/pigx-rnaseq-no-citeproc.patch | 33 |
3 files changed, 42 insertions, 2 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 71f1a25f83..110980bef0 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1601,6 +1601,7 @@ dist_patch_DATA = \ %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-rnaseq-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 150bbc361f..f5de16877e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10489,7 +10489,8 @@ once. This package provides tools to perform Drop-seq analyses.") "/pigx_rnaseq-" version ".tar.gz")) (sha256 (base32 - "1ja3bda1appxrzbfy7wp7khy30mm7lic8xbq3gkbpc5bld3as9cm")))) + "1ja3bda1appxrzbfy7wp7khy30mm7lic8xbq3gkbpc5bld3as9cm")) + (patches (search-patches "pigx-rnaseq-no-citeproc.patch")))) (build-system gnu-build-system) (arguments `(#:parallel-tests? #f ; not supported @@ -10502,6 +10503,9 @@ once. This package provides tools to perform Drop-seq analyses.") (substitute* "Makefile.in" (("^ tests/test_multiqc/test.sh") "") (("^ test.sh") "")))) + (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) @@ -10545,7 +10549,9 @@ once. This package provides tools to perform Drop-seq analyses.") ("python-deeptools" ,python-deeptools) ("python-pyyaml" ,python-pyyaml))) (native-inputs - `(("tzdata" ,tzdata))) + `(("tzdata" ,tzdata) + ("automake" ,automake) + ("autoconf" ,autoconf))) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for RNA sequencing experiments") (description "PiGX RNAseq is an analysis pipeline for preprocessing and diff --git a/gnu/packages/patches/pigx-rnaseq-no-citeproc.patch b/gnu/packages/patches/pigx-rnaseq-no-citeproc.patch new file mode 100644 index 0000000000..366ae3890a --- /dev/null +++ b/gnu/packages/patches/pigx-rnaseq-no-citeproc.patch @@ -0,0 +1,33 @@ +diff -Naur pigx_rnaseq-0.0.19/configure.ac pigx_rnaseq-0.0.19.patched/configure.ac +--- pigx_rnaseq-0.0.19/configure.ac 2021-07-23 14:01:00.304391428 +0200 ++++ pigx_rnaseq-0.0.19.patched/configure.ac 2021-10-06 13:51:29.512960106 +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([STAR], [STAR]) + find_or_override_prog([HISAT2], [hisat2]) + find_or_override_prog([HISAT2_BUILD], [hisat2-build]) +diff -Naur pigx_rnaseq-0.0.19/Makefile.in pigx_rnaseq-0.0.19.patched/Makefile.in +--- pigx_rnaseq-0.0.19/Makefile.in 2021-08-13 13:40:10.402922844 +0200 ++++ pigx_rnaseq-0.0.19.patched/Makefile.in 2021-10-06 13:51:04.052247524 +0200 +@@ -410,7 +410,6 @@ + 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_rnaseq-0.0.19/pigx-common/common/pigx-runner.in pigx_rnaseq-0.0.19.patched/pigx-common/common/pigx-runner.in +--- pigx_rnaseq-0.0.19/pigx-common/common/pigx-runner.in 2021-08-13 13:27:50.494352532 +0200 ++++ pigx_rnaseq-0.0.19.patched/pigx-common/common/pigx-runner.in 2021-10-06 13:51:38.798220108 +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'] |