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authorl-d-s <distefano.l@wehi.edu.au>2018-12-10 08:30:31 +1100
committerl-d-s <distefano.l@wehi.edu.au>2018-12-10 08:30:31 +1100
commit238c059743605853472d172f430227e06e20b891 (patch)
treeafd85c20c79467c52690b063d28b68f87927f69d /tools
parent25e9aae54ef8ae2b88a7ae677b4fd20d567e1a91 (diff)
gridss: fix tmpdir bug.
Diffstat (limited to 'tools')
-rw-r--r--tools/gridss-annotateVariants.nix1
-rw-r--r--tools/gridss-assemble.nix1
2 files changed, 2 insertions, 0 deletions
diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix
index 655b268..df3b1bd 100644
--- a/tools/gridss-annotateVariants.nix
+++ b/tools/gridss-annotateVariants.nix
@@ -55,6 +55,7 @@ stdenv.mkDerivation rec {
name = "gridss-identifyVariants";
buildInputs = [ jre ];
buildCommand = ''
+ TMPDIR=$(pwd)
ln -s ${ref} ref.fa
ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix
index 847830a..b24f742 100644
--- a/tools/gridss-assemble.nix
+++ b/tools/gridss-assemble.nix
@@ -39,6 +39,7 @@ stdenv.mkDerivation rec {
name = "gridss-assemble";
buildInputs = [ jre bwa ];
buildCommand = ''
+ TMPDIR=$(pwd)
ln -s ${ref} ref.fa
ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do