aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorJustin Bedo <cu@cua0.org>2018-11-29 11:52:42 +1100
committerJustin Bedo <cu@cua0.org>2018-11-29 11:52:42 +1100
commitdcb23a997359160ffdc58a971027fd77c45c7157 (patch)
tree7ba58bb0ea250ac999940ab3038fb4e6afb0ffaa
parent039b213f0a217f4787c04d40990006ee6d475173 (diff)
gridss: fix for nix installations outside of /nix
-rw-r--r--tools/gridss-annotateVariants.nix2
-rw-r--r--tools/gridss-assemble.nix2
-rw-r--r--tools/gridss-identifyVariants.nix2
3 files changed, 3 insertions, 3 deletions
diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix
index 122c451..adc4958 100644
--- a/tools/gridss-annotateVariants.nix
+++ b/tools/gridss-annotateVariants.nix
@@ -31,7 +31,7 @@ let
mkdir $WRKDIR
fi
for f in ${f attrs input}/* ; do
- ln -s $f $WRKDIR/$BASENAME.''${f#*.}
+ ln -s $f $WRKDIR/$BASENAME.''${f##*.}
done
'';
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix
index 9afb213..b61f28a 100644
--- a/tools/gridss-assemble.nix
+++ b/tools/gridss-assemble.nix
@@ -27,7 +27,7 @@ let
ln -s ${input} $WRKDIR/$BASENAME.sv.bam
ln -s ${bionix.samtools.index indexAttrs input} $WRKDIR/$BASENAME.sv.bai
for f in ${bionix.gridss.collectMetrics collectMetricsAttrs input}/* ; do
- ln -s $f $WRKDIR/$BASENAME.''${f#*.}
+ ln -s $f $WRKDIR/$BASENAME.''${f##*.}
done
'';
in
diff --git a/tools/gridss-identifyVariants.nix b/tools/gridss-identifyVariants.nix
index e5c74a4..d2dc665 100644
--- a/tools/gridss-identifyVariants.nix
+++ b/tools/gridss-identifyVariants.nix
@@ -30,7 +30,7 @@ let
mkdir $WRKDIR
fi
for f in ${f attrs input}/* ; do
- ln -s $f $WRKDIR/$BASENAME.''${f#*.}
+ ln -s $f $WRKDIR/$BASENAME.''${f##*.}
done
'';