• this repository was originally hosted at github.com/Benjamin-Vincent-Lab/Bowtie2 , moved here on 2/12/2024

This docker image sets up the environment to run Bowtie2 version 2.3.3.1

You will need an index reference to run this.

I built my refernce using this image by submitting as a slurm job via sbatch jobs/build_bowtie_index.job. At 16 threads and 4g per thread it took 24 minutes.

---- Helpful commands ----

Init:
cd /datastore/alldata/shiny-server/rstudio-common/dbortone/docker/bowtie2/; ls my_image=bowtie2_2.3.3.1:1

Run interactive session as root:
srun --pty -c 1 --mem 1g -p dockerbuild docker run -v /datastore:/datastore:shared -it dockerreg.bioinf.unc.edu:5000/${my_image} bash

Run interactive session as yoourself:
srun --pty -c 1 --mem 1g -p docker docker run -v /datastore:/datastore:shared -v /home/dbortone/scratch:/home/dbortone/scratch -it dockerreg.bioinf.unc.edu:5000/${my_image} bash

Build the image:
srun --pty -c 2 --mem 1g -w c6145-docker-2-0.local -p docker docker build -t dockerreg.bioinf.unc.edu:5000/${my_image} .

Push the image:
srun --pty -c 2 --mem 1g -w c6145-docker-2-0.local -p docker docker push dockerreg.bioinf.unc.edu:5000/${my_image}

Pull the image to other nodes:
srun --pty -c 1 --mem 1g -w r820-docker-2-0.local -p docker docker pull dockerreg.bioinf.unc.edu:5000/${my_image} srun --pty -c 1 --mem 1g -w r820-docker-2-1.local -p docker docker pull dockerreg.bioinf.unc.edu:5000/${my_image} srun --pty -c 1 --mem 1g -w fc830-docker-2-0.local -p docker docker pull dockerreg.bioinf.unc.edu:5000/${my_image} srun --pty -c 1 --mem 1g -w c6100-docker-2-0.local -p dockerbuild docker pull dockerreg.bioinf.unc.edu:5000/${my_image}

Check build works:
srun --pty -c 1 --mem 1g -p docker -w c6145-docker-2-0.local docker run -v /datastore:/datastore:shared dockerreg.bioinf.unc.edu:5000/bowtie2_2.3.3.1:1 bash -c "bowtie2-build --help"
srun --pty -c 1 --mem 1g -p docker -w c6145-docker-2-0.local docker run -v /datastore:/datastore:shared dockerreg.bioinf.unc.edu:5000/bowtie2_2.3.3.1:1 bash -c "bowtie2 --help"

Run a sample: sbatch jobs/test_sample.job