From e08e58209432b13f3270bd9dd858d1b7c2ef44ed Mon Sep 17 00:00:00 2001
From: wyleung <w.y.leung@e-sensei.nl>
Date: Tue, 4 Nov 2014 16:15:53 +0100
Subject: [PATCH] config json with executable used in biopet, SHARK specific
config
---
biopet-framework/examples/shark_apps.json | 48 +++++++++++++++++++++++
1 file changed, 48 insertions(+)
create mode 100644 biopet-framework/examples/shark_apps.json
diff --git a/biopet-framework/examples/shark_apps.json b/biopet-framework/examples/shark_apps.json
new file mode 100644
index 000000000..c0cdb33af
--- /dev/null
+++ b/biopet-framework/examples/shark_apps.json
@@ -0,0 +1,48 @@
+{
+ "mapping": {
+ "chunking": true,
+ "chunk_metrics": true,
+ "aligner": "bwa"
+ },
+ "bwa": {
+ "exe": "/usr/local/bwa/bwa-0.7.10/bwa",
+ "M": false
+ },
+ "seqtk": {
+ "exe":"/data/DIV5/SASC/common/programs/seqtk/seqtk/seqtk"
+ },
+ "sickle": {
+ "exe":"/data/DIV5/SASC/common/programs/sickle/sickle-1.33/sickle"
+ },
+ "clever": {
+ "exe": "/data/DIV5/SASC/common/programs/clever/clever-toolkit-v2.0rc3/bin/clever",
+ "version_exe": "/data/DIV5/SASC/common/programs/clever/clever-toolkit-v2.0rc3/bin/ctk-version"
+ },
+ "pindel": {
+ "exe": "/data/DIV5/SASC/common/programs/pindel/pindel-0.2.5/pindel"
+ },
+ "breakdancerconfig": {
+ "exe": "/data/DIV5/SASC/common/programs/breakdancer/breakdancer-v1.4.4/lib/breakdancer-max1.4.4/bam2cfg.pl",
+ "min_observations": 50000
+ },
+ "breakdancercaller": {
+ "exe": "/data/DIV5/SASC/common/programs/breakdancer/breakdancer-v1.4.4/bin/breakdancer-max",
+ "vmem": "6G"
+ },
+ "fastqc": {
+ "exe": "/usr/local/FastQC/FastQC_v0.10.1/fastqc"
+ },
+ "picard": {
+ "compressionlevel": 9
+ },
+ "seqstat": {
+ "exe": "/data/DIV5/SASC/common/programs/dQual/fastq-seqstat"
+ },
+ "stampy": {
+ "exe": "/usr/local/stampy/stampy-1.0.23/stampy.py",
+ "verbosity": 2
+ },
+ "sambamba": {
+ "exe": "/data/DIV5/SASC/common/programs/sambamba/sambamba-0.4.7/build/sambamba"
+ }
+}
--
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