From 847acc3206c34b45cabd4f5ae1465a576d7ef10a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 29 Mar 2022 13:42:48 +0200 Subject: gnu: pigx-rnaseq: Update to 0.0.20. * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.20. [source]: Remove patch. [inputs]: Add megadepth. * gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Remove patch. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/packages/patches/pigx-rnaseq-no-citeproc.patch | 33 ---------------------- 1 file changed, 33 deletions(-) delete mode 100644 gnu/packages/patches/pigx-rnaseq-no-citeproc.patch (limited to 'gnu/packages/patches') diff --git a/gnu/packages/patches/pigx-rnaseq-no-citeproc.patch b/gnu/packages/patches/pigx-rnaseq-no-citeproc.patch deleted file mode 100644 index 366ae3890a..0000000000 --- a/gnu/packages/patches/pigx-rnaseq-no-citeproc.patch +++ /dev/null @@ -1,33 +0,0 @@ -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'] -- cgit v1.2.3