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authorJustin Bedo <cu@cua0.org>2018-10-04 14:20:31 +1000
committerJustin Bedo <cu@cua0.org>2018-10-04 14:20:31 +1000
commitb51c2989b0d354ab96077c6af559dc20c026d42f (patch)
tree90b67ba7164214a0c0a4fba40f55c9bc4182e7d8 /tools
parent30d47b54b1e1ca63fb4a3bce26cc51a7b6017e23 (diff)
Refactor references
Diffstat (limited to 'tools')
-rw-r--r--tools/bwa-index.nix2
-rw-r--r--tools/bwa-mem.nix2
-rw-r--r--tools/gridss-callVariants.nix2
-rw-r--r--tools/platypus-callVariants.nix2
-rw-r--r--tools/samtools-faidx.nix1
-rw-r--r--tools/strelka-call.nix4
6 files changed, 7 insertions, 6 deletions
diff --git a/tools/bwa-index.nix b/tools/bwa-index.nix
index 3f9d385..48a2556 100644
--- a/tools/bwa-index.nix
+++ b/tools/bwa-index.nix
@@ -12,7 +12,7 @@ stdenv.mkDerivation {
name = "bwa-index";
buildInputs = [ bwa ];
buildCommand = ''
- ln -s ${ref} ref.fa
+ ln -s ${ref.seq} ref.fa
bwa index ${optionalString (flags != null) flags} ref.fa
mkdir $out
mv ref.fa.* $out
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index 6e83a6d..ca9e6a8 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -17,7 +17,7 @@ stdenv.mkDerivation {
name = "bwa-mem";
buildInputs = [ bwa bc ] ++ optional bamOutput samtools;
buildCommand = ''
- ln -s ${ref} ref.fa
+ ln -s ${ref.seq} ref.fa
for f in ${bionix.bwa.index indexAttrs ref}/* ; do
ln -s $f
done
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix
index e431560..c313c3f 100644
--- a/tools/gridss-callVariants.nix
+++ b/tools/gridss-callVariants.nix
@@ -19,7 +19,7 @@ stdenv.mkDerivation rec {
sha256 = "01srl3qvv060whqg1y1fpxjc5cwga5wscs1bmf1v3z87dignra7k";
};
buildCommand = ''
- ln -s ${ref} ref.fa
+ ln -s ${ref.seq} ref.fa
ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do
ln -s $f
diff --git a/tools/platypus-callVariants.nix b/tools/platypus-callVariants.nix
index c0204dc..7b68b28 100644
--- a/tools/platypus-callVariants.nix
+++ b/tools/platypus-callVariants.nix
@@ -16,7 +16,7 @@ in stdenv.mkDerivation {
name = "platypus";
buildInputs = [ platypus ];
buildCommand = ''
- ln -s ${ref} ref.fa
+ ln -s ${ref.seq} ref.fa
ln -s ${bionix.samtools.faix indexAttrs ref} ref.fa.fai
${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs}
${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
diff --git a/tools/samtools-faidx.nix b/tools/samtools-faidx.nix
index 72116b8..bf32bdf 100644
--- a/tools/samtools-faidx.nix
+++ b/tools/samtools-faidx.nix
@@ -9,6 +9,7 @@ with nixpkgs;
with lib;
stdenv.mkDerivation {
+
name = "samtools-faidx";
buildInputs = [ samtools ];
buildCommand = ''
diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index e7fbb58..ecdea84 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -19,8 +19,8 @@ in stdenv.mkDerivation {
name = "strelka";
buildInputs = [ strelka ];
buildCommand = ''
- ln -s ${ref} ref.fa
- ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
+ ln -s ${ref.seq} ref.fa
+ ln -s ${bionix.samtools.faidx indexAttrs ref.seq} ref.fa.fai
${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs}
${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}