Steffen Möller pushed to branch master at Debian Med / bcbio
Commits:
ffdc3278 by Steffen Moeller at 2021-05-07T23:55:11+02:00
Always use our Rscript.
- - - - -
5 changed files:
- debian/README.source
- debian/changelog
- debian/control
- + debian/patches/RscriptIsSystemVersion.patch
- debian/patches/series
Changes:
=====================================
debian/README.source
=====================================
@@ -4,5 +4,9 @@ bcbio for Debian
Please be aware that this package provides what upstream distributes
as bcbio-nextgen.
+debian/patches/RscriptIsSystemVersion.patch:
+ This Debian package should always work with Debian's Rscript since
+ we have also installed our R modules with the system.
+
-- Steffen Moeller <moel...@debian.org> Sun, 11 Feb 2018 18:40:28 +0100
=====================================
debian/changelog
=====================================
@@ -4,6 +4,7 @@ bcbio (1.2.8-1) UNRELEASED; urgency=medium
* Standards-Version: 4.5.1 (routine-update)
* Removed now obsolete patch on abc collections
* Updated dependencies
+ * Point to system version of Rscript - always
-- Steffen Moeller <moel...@debian.org> Fri, 07 May 2021 20:29:57 +0200
=====================================
debian/control
=====================================
@@ -56,13 +56,15 @@ Build-Depends: debhelper-compat (= 13),
pythonpy <!nocheck>,
rapmap <!nocheck>,
rna-star <!nocheck>,
- r-other-wasabi <!nocheck>,
+ r-base-core <!nocheck>,
r-bioc-htsfilter <!nocheck>,
r-bioc-degreport <!nocheck>,
r-bioc-purecn <!nocheck>,
+ r-bioc-summarizedexperiment <!nocheck>,
r-cran-tidyverse <!nocheck>,
r-bioc-titancna <!nocheck>,
r-bioc-tximport <!nocheck>,
+ r-other-wasabi <!nocheck>,
salmon <!nocheck>,
samblaster <!nocheck>,
samtools <!nocheck>,
@@ -182,6 +184,8 @@ Suggests: toil,
tophat2,
# found in source code but not exactly sure about its importance
tophat-recondition,
+ r-bioc-summarizedexperiment,
+ r-cran-tidyverse,
r-other-wasabi
Description: toolkit for analysing high-throughput sequencing data
This package installs the command line tools of the bcbio-nextgen
=====================================
debian/patches/RscriptIsSystemVersion.patch
=====================================
@@ -0,0 +1,33 @@
+Author: Steffen Moeller <moel...@debian.org>
+Description: With Debian we want to use _our_ R installation, while with the
+ typical conda-installation of bcbio this is the other way around. It is
+ important not to mix these up, hence this strict return of the sytem
+ version.
+ This patch is not meant to be sent upstream.
+
+Index: bcbio/bcbio/utils.py
+===================================================================
+--- bcbio.orig/bcbio/utils.py
++++ bcbio/bcbio/utils.py
+@@ -694,18 +694,11 @@ def dictapply(d, fn):
+ return d
+
+ def Rscript_cmd(env="base"):
+- """Retrieve path to locally installed Rscript in the given env.
++ """Original bcbio: Retrieve path to locally installed Rscript in the
given env.
+ Prefers Rscript version installed via conda to a system version.
++ Debian: We use ours.
+ """
+- if env == "base":
+- rscript = which(os.path.join(get_bcbio_bin(), "Rscript"))
+- else:
+- conda_dir = get_conda_dir()
+- rscript = os.path.join(conda_dir, "envs", env, "bin", "Rscript")
+- if rscript:
+- return rscript
+- else:
+- return which("Rscript")
++ return "/usr/bin/Rscript"
+
+ def R_sitelib(env="base"):
+ """Retrieve the R site-library installed with the bcbio installer for a
given
=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ pythonpaths.patch
hts_nim_tools.patch
cnvkitPath.patch
fixeFreetypePreload.patch
+RscriptIsSystemVersion.patch
View it on GitLab:
https://salsa.debian.org/med-team/bcbio/-/commit/ffdc327858cbedf8bd9d3d7f1a777cdebac537e7
--
View it on GitLab:
https://salsa.debian.org/med-team/bcbio/-/commit/ffdc327858cbedf8bd9d3d7f1a777cdebac537e7
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