From 238c059743605853472d172f430227e06e20b891 Mon Sep 17 00:00:00 2001
From: l-d-s <distefano.l@wehi.edu.au>
Date: Mon, 10 Dec 2018 08:30:31 +1100
Subject: gridss: fix tmpdir bug.

---
 tools/gridss-annotateVariants.nix | 1 +
 tools/gridss-assemble.nix         | 1 +
 2 files changed, 2 insertions(+)

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
-- 
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