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wwylab / MuSE

Somatic point mutation caller
GNU General Public License v2.0
18 stars 6 forks source link

Request: Make Docker container available #21

Closed famosab closed 1 day ago

famosab commented 1 month ago

Related to my other issue #20. Thanks for including the Dockerfile. Would it be possible to update the biocontainers container?

jiyunmaths commented 1 month ago

@famosab , thank you for your suggestions. Actually there is a docker container available at DockerHub. Would you like to have a try https://hub.docker.com/repository/docker/jiyunmathbham/muse2/general ? For the conda package, we are considering to create it. It may take some time.

famosab commented 1 month ago

Thanks for pointing me to the container! I am just building one with the latest version (2.1) and it seems that yours is a bit older. Maybe you can link it in the README anyways!

famosab commented 1 month ago

Also I cant install as described in the README neither on my mac nor on out workstation (linux based). I am trying your docker container now, but so far the command MuSE is always not found :(

jiyunmaths commented 1 month ago

@famosab , I have updated the docker container of MuSE to the latest version. Please check: https://hub.docker.com/repository/docker/jiyunmathbham/muse2/general.

I tested the container on our Linux server and found no issue. I was using singularity in stead of docker since docker requires root permission which I do not have. My commands are below:

## singularity 3.7.0 or above

singularity pull --arch amd64 muse2.sif docker://jiyunmathbham/muse2:latest 
bam_dir=directory_of_the_bam_files_of_tumor_and_normal/
reference=directory_of_reference_genome_and_dbsnp/ # such as Homo_sapiens_assembly38.fasta and Homo_sapiens_assembly38.dbsnp138.vcf.gz

# MuSE call
singularity run --bind $bam_dir:/bam/,$reference:/reference/ muse2.sif /MuSE-2.1/MuSE call -f /reference/Homo_sapiens_assembly38.fasta -O $bam_dir/tumor_normal -n 5 /bam/tumor.bam /bam/normal.bam

# MuSE sump
singularity run --bind $bam_dir:/bam/,$reference:/reference/ muse2.sif /MuSE-2.1/MuSE sump -I /bam/tumor_normal.MuSE.txt -O /bam/tumor_normal.vcf -E -n 5 -D /reference/Homo_sapiens_assembly38.dbsnp138.vcf.gz

Please try the above command and let me know if it does not work on your machine. Thanks.