diff options
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 12 | ||||
| -rw-r--r-- | gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch | 33 |
3 files changed, 3 insertions, 43 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index f5e2702031..420aa91d86 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1627,7 +1627,6 @@ 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-scrnaseq-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 eed7e54f7f..3ad8800fdb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11132,7 +11132,7 @@ methylation and segmentation.") (define-public pigx-scrnaseq (package (name "pigx-scrnaseq") - (version "1.1.7") + (version "1.1.8") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" @@ -11140,20 +11140,14 @@ methylation and segmentation.") "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx")) - (patches (search-patches "pigx-scrnaseq-no-citeproc.patch")))) + "1lc42hl8mz95kilh0z39s3wnv092mhm6vl2i394n0yfvdzk4f885")))) (build-system gnu-build-system) (arguments - `(#:phases + '(#:phases (modify-phases %standard-phases - (add-before 'bootstrap 'autoreconf - (lambda _ - (invoke "autoreconf" "-vif"))) (add-before 'configure 'set-PYTHONPATH (lambda _ (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))))) - (native-inputs - (list automake autoconf)) (inputs `(("coreutils" ,coreutils) ("perl" ,perl) diff --git a/gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch b/gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch deleted file mode 100644 index 4cce33fb01..0000000000 --- a/gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch +++ /dev/null @@ -1,33 +0,0 @@ -diff -Naur pigx_scrnaseq-1.1.7/configure.ac pigx_scrnaseq-1.1.7.patched/configure.ac ---- pigx_scrnaseq-1.1.7/configure.ac 2020-03-17 14:37:46.000000000 +0100 -+++ pigx_scrnaseq-1.1.7.patched/configure.ac 2021-10-06 13:55:49.779271317 +0200 -@@ -43,7 +43,6 @@ - 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([STAR], [STAR]) - find_or_override_prog([SAMTOOLS], [samtools]) -diff -Naur pigx_scrnaseq-1.1.7/Makefile.in pigx_scrnaseq-1.1.7.patched/Makefile.in ---- pigx_scrnaseq-1.1.7/Makefile.in 2020-11-30 16:55:48.000000000 +0100 -+++ pigx_scrnaseq-1.1.7.patched/Makefile.in 2021-10-06 13:55:52.224340194 +0200 -@@ -395,7 +395,6 @@ - PACKAGE_URL = @PACKAGE_URL@ - PACKAGE_VERSION = @PACKAGE_VERSION@ - PANDOC = @PANDOC@ --PANDOC_CITEPROC = @PANDOC_CITEPROC@ - PATH_SEPARATOR = @PATH_SEPARATOR@ - PERL = @PERL@ - PYTHON = @PYTHON@ -diff -Naur pigx_scrnaseq-1.1.7/pigx-scrnaseq.in pigx_scrnaseq-1.1.7.patched/pigx-scrnaseq.in ---- pigx_scrnaseq-1.1.7/pigx-scrnaseq.in 2020-11-30 16:08:55.000000000 +0100 -+++ pigx_scrnaseq-1.1.7.patched/pigx-scrnaseq.in 2021-10-06 13:55:47.889218079 +0200 -@@ -274,7 +274,6 @@ - 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'] |