# HG changeset patch
# User stef
# Date 1412950435 14400
# Node ID b51c36920d7b9cde9a940956e3da6bd1430988bf
# Parent  12f7ce7de71f8799f5f3b15d89717dc14114c55a
Uploaded

diff -r 12f7ce7de71f -r b51c36920d7b falco/misc/init.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/falco/misc/init.sh	Fri Oct 10 10:13:55 2014 -0400
@@ -0,0 +1,57 @@
+#!/bin/bash
+
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+index=/ccagc/data/ref/hg19/stampy/hg19
+hash=/ccagc/data/ref/hg19/stampy/hg19
+faref=/ccagc/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa
+bwaref=/ccagc/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa
+#manifest=/ccagc/data/ref/manifests/TSACP/TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt
+#targetBed=/ccagc/data/ref/manifests/TSACP/TSACP.bed
+
+dbSnp=/ccagc/data/ref/dbSNP/common_no_known_medical_impact_00-latest.f.vcf
+dbNSFP=/ccagc/data/ref/dbNSFP/dbNSFP2.0b3.txt
+clinvar=/ccagc/data/ref/dbSNP/clinvar_00-latest.f.vcf
+cosmic=/ccagc/data/ref/cosmic/CosmicCodingMuts_v64_26032013_noLimit_wgs.f.vcf
+cosmicNC=/ccagc/data/ref/cosmic/CosmicNonCodingVariants_v64_26032013_noLimit_wgs.f.vcf
+locifilt=/ccagc/data/ref/dbSNP/locifilt.tsv
+canonicals=/ccagc/data/ref/manifests/TSACP/canonicals.tsv
+
+illmP5="AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC"
+illmP7="AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT"
+
+adapt_clipper=/ccagc/lib/cutadapt/cutadapt-1.1/bin/cutadapt
+qTrim=/ccagc/bin/fastq_quality_trimmer
+stampy=/ccagc/lib/stampy/stampy-1.0.18/stampy.py
+#samtools=/ccagc/lib/samtools/samtools-0.1.18/samtools
+#bcftools=/ccagc/lib/samtools/samtools-0.1.18/bcftools/bcftools
+snpEff=/ccagc/lib/snpEff/snpEff_3_0a
+snpEff=/ccagc/lib/snpEff/snpEff_v3_4
+snpSift=/ccagc/lib/SnpSift
+
+varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar
+java=/usr/bin/java
+bwa=/ccagc/lib/bwa/bwa-0.5.9/bwa
+flash=/ccagc/lib/flash/FLASH-1.2.2/flash
+
+pairUp=$DIR/misc/pairUp.pl
+pileup2cov=$DIR/misc/pileup2cov.pl
+pileup2cov2=$DIR/misc/perAmpliconAnalysis.pl
+addQual=$DIR/misc/addQual.R
+
+qc2vcf=$DIR/misc/qc2vcf.pl
+qcFilt=$DIR/misc/qcFilt.pl
+plots=$DIR/misc/plots.R
+plotsPng=$DIR/misc/plotsPng.R
+
+attachManifest=$DIR/misc/attachManifest.pl
+plots=$DIR/misc/plots.R
+VcAn=$DIR/amplicon-VcAn-TSACP.sh
+report=$DIR/amplicon-Report.sh
+
+alignmentStats=$DIR/misc/alignmentStats.pl
+errorRate=$DIR/misc/errorRate.pl
+plotQc=$DIR/misc/plotsQC.R
+
+#export PATH=$PATH:/ccagc/lib/samtools/samtools-0.1.18/
+source ./galaxy_init.sh