From e5fa8f07e51422d2b07f4acb8154e2c2a90dc2fa Mon Sep 17 00:00:00 2001
From: wyleung <w.y.leung@e-sensei.nl>
Date: Tue, 4 Nov 2014 16:29:32 +0100
Subject: [PATCH] Removed apps config, let the user decide on the settings
---
biopet-framework/examples/shark_apps.json | 15 ++++-----------
1 file changed, 4 insertions(+), 11 deletions(-)
diff --git a/biopet-framework/examples/shark_apps.json b/biopet-framework/examples/shark_apps.json
index c3f06bd50..d5bd63e02 100644
--- a/biopet-framework/examples/shark_apps.json
+++ b/biopet-framework/examples/shark_apps.json
@@ -1,7 +1,6 @@
{
"bwa": {
- "exe": "/usr/local/bwa/bwa-0.7.10/bwa",
- "M": false
+ "exe": "/usr/local/bwa/bwa-0.7.10/bwa"
},
"seqtk": {
"exe":"/data/DIV5/SASC/common/programs/seqtk/seqtk/seqtk"
@@ -17,25 +16,19 @@
"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
+ "exe": "/data/DIV5/SASC/common/programs/breakdancer/breakdancer-v1.4.4/lib/breakdancer-max1.4.4/bam2cfg.pl"
},
"breakdancercaller": {
- "exe": "/data/DIV5/SASC/common/programs/breakdancer/breakdancer-v1.4.4/bin/breakdancer-max",
- "vmem": "6G"
+ "exe": "/data/DIV5/SASC/common/programs/breakdancer/breakdancer-v1.4.4/bin/breakdancer-max"
},
"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
+ "exe": "/usr/local/stampy/stampy-1.0.23/stampy.py"
},
"sambamba": {
"exe": "/data/DIV5/SASC/common/programs/sambamba/sambamba-0.4.7/build/sambamba"
--
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