• This repository was initially hosted at github.com/Benjamin-Vincent-Lab/trust , moved on 2/12/2024

This docker image sets up the environment to run TRUST version 3.0.1

This needs to be run on bam files. Theyu previously recommended Bowtie2 or MapSlice to run the bams so I would suggest making your bams with those to avoid having to optomize parameters for STAR.
https://bitbucket.org/liulab/trust

---- Helpful commands ----

Init:
cd /datastore/alldata/shiny-server/rstudio-common/dbortone/docker/trust/; ls my_image=trust_3.0.3:1

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/trust_3.0.1:1 bash -c "export HOME=/tmp; trust --help"

srun --pty -c 8 --mem 16g -p docker bash
num_threads=8
cd /home/dbortone/scratch/test_bowtie
sam_file=test_file.sam
trust_bam_file=test_file_bowtie2.bam
samtools view -@ $num_threads -S -b $sam_file > unsorted_$trust_bam_file
samtools sort -@ $num_threads -o $trust_bam_file unsorted_$trust_bam_file
samtools index -@ $num_threads $trust_bam_file
exit

srun --pty -c 8 --mem 16g -p docker -w c6145-docker-2-0.local docker run -v /datastore:/datastore:shared -v /home/dbortone:/home/dbortone dockerreg.bioinf.unc.edu:5000/trust_3.0.1:1 bash -c "export HOME=/tmp; trust --help"

`srun --pty -c 8 --mem 16g -p docker -w c6145-docker-2-0.local docker run -v /datastore:/datastore:shared -v /home/dbortone:/home/dbortone dockerreg.bioinf.unc.edu:5000/trust_3.0.1:1 bash -c "\
trust \
--CoreN=8 \
--genome=hg38 \
-H \
-E \
-f /home/dbortone/scratch/test_bowtie/test_file_bowtie2.bam \
-o /home/dbortone/scratch/test_bowtie/"