We’ve offered the following installation guide for users who prefer installing the Anaconda Environment manually.

Step 1: Clone Github Repository

$ git clone https://github.com/BioHPC/SLUPipe.git

Step 2: Create an Anaconda Environment

$ conda create -n SLUPipe

Step 3: Activate the Anaconda Environment:

$ source activate SLUPipe

Step 4: Install Python Packages Needed for SLUPipe

biobambam-2.0.87

$ conda install -c bioconda biobambam

bwa.kit-0.7.15

$ conda install -c bioconda bwakit

ensembl-vep 95.3

$ conda install -c bioconda ensembl-vep=95.3

GenomeAnalysisTK-3.8.0

$ conda install -c bioconda gatk

MuSE 1.0.rc

$ conda install -c bioconda muse

pandas 0.24.2

$ conda install -c anaconda pandas

pindel-0.2.5b9

$ conda install -c bioconda pindel

platypus-opt 1.0.3

$ conda install -c bioconda platypus-variant

psycopg2 - 2.7.6.1

$ conda install -c anaconda psycopg2

samtools-1.9

$ conda install -c bioconda samtools

strelka 2.9.10

$ conda install -c bioconda strelka

somatic-sniper 1.0.5.0

$ conda install -c bioconda somatic-sniper

varscan - 2.4.3.2

$ conda install -c bioconda varscan

vcf2maf - 1.6.16

$ conda install -c bioconda vcf2maf

Step 6. Configure Ensembl VEP For Variant Annotation & MAF Conversion (Local Cache Installation):

  1. Create .vep directory to store offline cache: mkdir ~/.vep
  2. $ cd $HOME/.vep
  3. $ curl -O -C - ftp://ftp.ensembl.org/pub/release-95/variation/indexed_vep_cache/homo_sapiens_vep_95_GRCh38.tar.gz
  4. $ tar xzf homo_sapiens_vep_96_GRCh38.tar.gz

Please Note: Download time will vary depending on time of day (1 Hr+)

Step 7: Copying Strelka 2 Configuration File to SLUPipe Working Directory:

  1. Locate “configureStrelkaSomaticWorkflow.py” found in SLUPipe conda env bin directory (~/.conda/envs/SLUPipe/bin)
  2. Copy file into SLUPipe working directory ($SLUPipe/src)
   $ cp ~/.conda/envs/SLUPipe/bin/configureStrelkaSomaticWorkflow.py $SLUPipe/src/

Please Note: $SLUIPipePATH is your current working directory (user can check this by typing “pwd” in terminal)

Tip: If unable to locate ./conda/envs/SLUPipe/bin directory, please run the following two commands to locate path:

$ source activate SLUPipe (start SLUPipe environment)
$ which python (prints full path related to SLUPipe conda environment)

Step 8: Add .fasta, .fai, dnSNP, normal panels files to src/referenceFiles directory.

GATK Tutorial Data 9183 Somatic Variants: https://drive.google.com/drive/folders/1QdtVEronIzs04L37BFkw29TLjNWcyOpf

  1. 1kg_40_m2pon_sitesonly_subset50k.vcf
  2. 1kg_40_m2pon_sitesonly_subset50k.vcf.gz
  3. 1kg_40_m2pon_sitesonly_subset50k.vcf.idx
  4. 1kg_40_m2pon_sitesonly_subset50k.vcf.gz.tbi
  5. dbSNP142_GRCh38_subset50k.vcf.gz
  6. dbSNP142_GRCh38_subset50k.vcf
  7. dbSNP142_GRCh38_subset50k.vcf.idx
  8. dbSNP142_GRCh38_subset50k.vcf.gz.tbi

GATK Resource Bundle: https://software.broadinstitute.org/gatk/download/bundle

  1. Homo_sapiens_assembly38.dict
  2. Homo_sapiens_assembly38.fasta.index
  3. Homo_sapiens_assembly38.fasta.fai
  4. Homo_sapiens_assembly38.fasta