From dcb23a997359160ffdc58a971027fd77c45c7157 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 29 Nov 2018 11:52:42 +1100
Subject: gridss: fix for nix installations outside of /nix

---
 tools/gridss-annotateVariants.nix | 2 +-
 tools/gridss-assemble.nix         | 2 +-
 tools/gridss-identifyVariants.nix | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

(limited to 'tools')

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
   '';
 
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