Dependencies

Dependency	Version	Handlers
BCFtools	0.2.0	Variant_Analysis
Bedtools	2.17.0	Coverage_Mapping
Burrows-Wheeler Aligner (BWA)	0.7.15	Read_Mapping
Enthought Python Distribution	1.5.2	Variant_Analysis
FastQC	0.11.5	Quality_Assessment
Fastx Toolkit	0.0.14	GBS Demultiplexing
GATK	3.8.0	Haplotype_Caller, Genotype_GVCFs, Variant_Recalibrator
GNU Parallel	20160822	Quality_Assessment, Adapter_Trimming, Quality_Trimming, SAM_Processing (SAMtools), Coverage_Mapping, Create_HC_Subset, Variant_Recalibrator, Variant_Analysis
Java	1.8	SAM_Processing (Picard), Haplotype_Caller, Genotype_GVCFs, Variant_Recalibrator
molpopgen	Commit b5ee78e	Variant_Analysis
Picard	2.9.0	SAM_Processing (Picard), all GATK handlers (only if the reference is missing a dictionary file)
Portable Batch System (PBS)	4.2.9	All Handlers
Python	3.6.1	Create_HC_Subset, Variant_Recalibrator, Variant_Filtering, Variant_Analysis
R	3.3.1	Quality_Trimming, Coverage_Mapping, Create_HC_Subset, Variant_Filtering
Riss-util	1.0	Quality_Assessment
SAMTools	1.3.1	SAM_Processing (SAMtools and Picard)
Scythe	Commit 20d3cff	Adapter_Trimming
Seqqs	Commit 3d05375	Quality_Trimming
Sickle	1.33	Quality_Trimming
TeX Live	20131202	Variant_Analysis
VCFtools	0.1.14	Create_HC_Subset, Variant_Recalibrator, Variant_Filtering, Variant_Analysis
vcflib	1.0.0	Create_HC_Subset, Variant_Filtering, Variant_Analysis

If running sequence_handling on the Minnesota Supercomputing Institute, all dependencies are already installed with the correct version. Make sure that every line that starts with module load at the bottom of the configuration file is uncommented and that you have access to the Morrell Lab modules. To gain access to the Morrell Lab modules, please run the following command on the login host:

echo export MODULEPATH=/panfs/roc/groups/9/morrellp/public/Modules:'$MODULEPATH' >> ~/.bash