From 23c1b898d8f651e3c67b4f04e4d4a94a893e5d87 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Fri, 7 Feb 2020 11:19:23 +0100
Subject: [PATCH] Bypass error from bedGraphToBigWig
---
singularity/workflows_base.def | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/singularity/workflows_base.def b/singularity/workflows_base.def
index a5af84f..9327a88 100644
--- a/singularity/workflows_base.def
+++ b/singularity/workflows_base.def
@@ -94,7 +94,8 @@ From:python:3.7-buster
rsync -azvP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin/.
prog="bedGraphToBigWig"
echo "# ${prog}" >> /usr/local/share/doc/program_versions.txt
- eval "${prog}" 2>> /usr/local/share/doc/program_versions.txt
+ # `|| :` is to "ignore" error exit code from bedGraphToBigWig
+ eval "${prog}" 2>&1 | head -1 >> /usr/local/share/doc/program_versions.txt || :
# It is possible to test whether the R install is already OK
deb_source="deb http://cran.irsn.fr/bin/linux/debian buster-cran35/"
echo ${deb_source} >> /etc/apt/sources.list.d/cran.list
--
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