rnaseq_pipeline_config.txt

SINGULARITY             /opt/local/singularity/2.6.0/bin
BOWTIE2			/opt/common/CentOS_6/bowtie2/bowtie2-2.2.4
BOWTIE			/opt/common/CentOS_6/bowtie/bowtie-1.1.1
CHIMERASCAN		/opt/common/CentOS_6/chimerascan/chimerascan-0.4.5/chimerascan
CUFFLINKS		/opt/common/CentOS_6/cufflinks/cufflinks-2.2.1.Linux_x86_64
CUTADAPT		/opt/common/CentOS_6/cutadapt/cutadapt-1.6/bin
DEFUSE			/opt/common/CentOS_6/defuse/defuse-0.6.2
DEXSEQ			/opt/common/CentOS_6/dexseq/DEXSeq_1.12.1
EXPRESS			/opt/common/CentOS_6/express/express-1.5.1-linux_x86_64
FUSIONCATCHER		/opt/common/CentOS_6/fusioncatcher/fusioncatcher_v0.99.3e
HTSEQ			/opt/common/CentOS_6/htseq/HTSeq-0.5.3/scripts
KALLISTO		/opt/common/CentOS_6/kallisto/kallisto_linux-v0.42.1
JAVA			/opt/common/CentOS_6/java/jdk1.7.0_75/bin
MAPSPLICE		/opt/common/CentOS_6/mapsplice/MapSplice-v2.1.8
PERL			/opt/common/CentOS_6/perl/perl-5.22.0/bin
PICARD			/opt/common/CentOS_6/picard/picard-tools-1.124
PYTHON			/opt/common/CentOS_6/python/python-2.7.8/bin
SINGULARITY_R		/opt/common/CentOS_6/R/R-4.0.0/bin
R			/juno/opt/common/bic/R/R-4.0.2/bin
RSEM			/opt/common/bic/rsem/RSEM-1.3.3
SAMTOOLS		/opt/common/CentOS_6/samtools/samtools-0.1.19
STAR			/opt/common/CentOS_6/star/STAR-STAR_2.5.0a/bin/Linux_x86_64
STAR_FUSION		/opt/common/CentOS_6/STAR-Fusion/STAR-Fusion_v0.5.4/STAR-Fusion-master
TOPHAT			/opt/common/CentOS_6/tophat/tophat-2.0.14.Linux_x86_64