Ir para o conteúdo

Environment Setup

Pipeline data

All the files needed for the hands-on activity are stored in the directory shown below:

tree $HOME/environment/hands-on
├── bin
   └── gghist.R
├── data
   ├── blacklist.bed
   ├── genome.fa
   ├── known_variants.vcf.gz
   └── reads
       ├── ENCSR000COQ1_1.fastq.gz
       ├── ENCSR000COQ1_2.fastq.gz
       ├── ENCSR000COQ2_1.fastq.gz
       ├── ENCSR000COQ2_2.fastq.gz
       ├── ENCSR000COR1_1.fastq.gz
       ├── ENCSR000COR1_2.fastq.gz
       ├── ENCSR000COR2_1.fastq.gz
       ├── ENCSR000COR2_2.fastq.gz
       ├── ENCSR000CPO1_1.fastq.gz
       ├── ENCSR000CPO1_2.fastq.gz
       ├── ENCSR000CPO2_1.fastq.gz
       └── ENCSR000CPO2_2.fastq.gz
├── nextflow.config

3 directories, 19 files

Pulling the Docker image

Nextflow can pull Docker images at runtime, but let’s just download it manually to see how Docker works:

docker pull cbcrg/callings-with-gatk:latest

You should see the progress of the download:

sha256:93910bf77bc197cb790eca776e42950bc8eff117bdc6e67157295e09c98fc381: Pulling from cbcrg/callings-with-gatk
915665fee719: Downloading [=============================================>     ] 47.08 MB/51.36 MB
f332de2321e6: Downloading [===========>                                       ] 41.96 MB/187.8 MB
1577a6dd9e43: Downloading [===============================>                   ] 46.72 MB/73.45 MB
7059d9bb5245: Waiting
71863f70269f: Waiting
ce2a2879246d: Waiting
e38ba5d5f9fb: Waiting
90158da87bb2: Waiting

and the following message when the pull is completed:

Digest: sha256:93910bf77bc197cb790eca776e42950bc8eff117bdc6e67157295e09c98fc381
Status: Downloaded newer image for cbcrg/callings-with-gatk:latest

Script permission

Make sure the following R script has execute permissions:

chmod +x $HOME/environment/hands-on/bin/gghist.R