diff options
| author | Justin Bedo <cu@cua0.org> | 2018-11-29 11:52:42 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-11-29 11:52:42 +1100 |
| commit | dcb23a997359160ffdc58a971027fd77c45c7157 (patch) | |
| tree | 7ba58bb0ea250ac999940ab3038fb4e6afb0ffaa | |
| parent | 039b213f0a217f4787c04d40990006ee6d475173 (diff) | |
gridss: fix for nix installations outside of /nix
| -rw-r--r-- | tools/gridss-annotateVariants.nix | 2 | ||||
| -rw-r--r-- | tools/gridss-assemble.nix | 2 | ||||
| -rw-r--r-- | tools/gridss-identifyVariants.nix | 2 |
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 ''; |