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Author: Steffen Moeller <moeller@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
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