I update several settings to let the vcf pipeline share the same docker container with RNA pipeline. The update is in the update_docker branch.
@amcooksey , could you check if the new Docker settings are compatible with SCINet?
Also, @g8tor , could you help me with the code review? Thank you both for your help.
The changes are below:
Change apt-get to apt and add --no-install-recommends flag
Update tools' version and add tools in Dockerfile:
a. update openjdk to 17
b. add cwl runner (cwltool)
c. add tabix for indexing vcf file
d. add several prerequisites for regtools, including:
gfortran, libreadline-dev, libpcre3-dev, build-essential, and libnss-sss
e. update samtools to 1.17
f. update sratoolkit to 3.0.2
g. add bwa
Remove the compressed file after installing the tools in Dockerfile.
Setting the tools let can be accessed directly from the shell:
a. gatk
b. FastQC
c. picard
d. trimmomatic
Update tools in setup.py file, including:
a. update FastQC to v0.12.1
b. update Trimmomatic to 0.39
c. update picard to 3.0.0
d. updaate gatk to 4.4.0.0
I update several settings to let the vcf pipeline share the same docker container with RNA pipeline. The update is in the update_docker branch. @amcooksey , could you check if the new Docker settings are compatible with SCINet? Also, @g8tor , could you help me with the code review? Thank you both for your help.
The changes are below: