For user convenience, SLUPipe has been developed using Anaconda Environments.

Please Note: If problems have appeared installing SLUPipe, please head to the manual installation.

Installation Steps

Step 1: Clone Github Repository

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

Step 2: Create SLUPipe Anaconda environment.

$ cd SLUPipe
$ conda env create -f environment.yml (environment.yml can be found in SLUPipe root directory)

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

Please Note: Environment creation will take around 30-45 minutes to complete.

Step 3: Configure Ensembl VEP For Variant Annotation & MAF Conversion (Local Cache Installation): Create .vep directory at your home directory ($HOME) to store offline cache.

  1. $ cd ~ (Takes you to your home directory. You can also use cd $HOME as well)
  2. $ mkdir .vep
  3. $ cd .vep
  4. $ curl -O -C - ftp://ftp.ensembl.org/pub/release-95/variation/indexed_vep_cache/homo_sapiens_vep_95_GRCh38.tar.gz
  5. $ tar xzf homo_sapiens_vep_96_GRCh38.tar.gz

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

Step 4: Copying Strelka 2 Configuration File to SLUPipe Working Directory:

  1. Locate “configureStrelkaSomaticWorkflow.py” found in 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/

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 5: 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

Please Note: If problems have appeared installing SLUPipe, please head to the manual installation.