diff options
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 10 | ||||
| -rw-r--r-- | gnu/packages/patches/pigx-bsseq-no-citeproc.patch | 33 |
3 files changed, 42 insertions, 2 deletions
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'] |