Merge branch 'feature-sharkapps' into 'develop'

Feature sharkapps

sample config file, which should be used by everyone during development.

See merge request !41

biopet-framework/examples/shark_apps.json

+{
+    "bwa": {
+        "exe": "/usr/local/bwa/bwa-0.7.10/bwa"
+    },
+    "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"
+    },
+    "breakdancercaller": {
+        "exe": "/data/DIV5/SASC/common/programs/breakdancer/breakdancer-v1.4.4/bin/breakdancer-max"
+    },
+    "fastqc": {
+        "exe": "/usr/local/FastQC/FastQC_v0.10.1/fastqc"
+    },
+    "seqstat": {
+        "exe": "/data/DIV5/SASC/common/programs/dQual/fastq-seqstat"
+    },
+    "stampy": {
+        "exe": "/usr/local/stampy/stampy-1.0.23/stampy.py"
+    },
+    "sambamba": {
+        "exe": "/data/DIV5/SASC/common/programs/sambamba/sambamba-0.4.7/build/sambamba"
+    }
+}