[med-svn] [Git][med-team/bcbio][master] Always use our Rscript.

[Steffen Möller]

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 <moeller at 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 <moeller at 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 <moeller at 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

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View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/ffdc327858cbedf8bd9d3d7f1a777cdebac537e7
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