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| author | l-d-s <distefano.l@wehi.edu.au> | 2018-12-10 08:30:31 +1100 |
|---|---|---|
| committer | l-d-s <distefano.l@wehi.edu.au> | 2018-12-10 08:30:31 +1100 |
| commit | 238c059743605853472d172f430227e06e20b891 (patch) | |
| tree | afd85c20c79467c52690b063d28b68f87927f69d /tools | |
| parent | 25e9aae54ef8ae2b88a7ae677b4fd20d567e1a91 (diff) | |
gridss: fix tmpdir bug.
Diffstat (limited to 'tools')
| -rw-r--r-- | tools/gridss-annotateVariants.nix | 1 | ||||
| -rw-r--r-- | tools/gridss-assemble.nix | 1 |
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 |