Issue regarding package version conflict

[Yifan-bio]

Hi, thank you for developing this tool which ease many of the processing issues.

With regards to the installation using conda, I have encountered serveral package to be depending of different version of pysam. dysgu 1.6.2. requires pysam==0.21.0 while truvari requires >0.22. The following is the error I got by running the conda installation command (/package/SpecImmune-0.0.2$ mamba env create -n SpecImmune -f environment.yml):
The conflict is caused by:
The user requested pysam==0.21.0
cutesv 2.1.2 depends on pysam
dysgu 1.6.2 depends on pysam==0.21.0
genomeview 1.1.4 depends on pysam
truvari 5.2.0 depends on pysam>=0.22

Thank you

[wshuai294]

Hi, thanks for reporting this. The conflict comes from dysgu 1.6.2 requiring pysam==0.21.0 while truvari requires pysam>=0.22, so they can’t be satisfied in one env.

We’ve updated the installation to avoid that:

dysgu was removed from the pip: section of environment.yml, so the env can be created with pysam 0.23 (compatible with truvari and the rest of the pipeline).
After creating and activating the env, install dysgu without its dependency pin:

mamba env create -n SpecImmune -f environment.yml
mamba activate SpecImmune
pip install --no-deps dysgu==1.6.2

This keeps pysam at 0.23 and adds dysgu; the pipeline is tested with this combination.
Please pull the latest environment.yml and follow the steps above. If you still hit any issue, tell us the exact command and error message and we’ll follow up.

Thanks again for trying SpecImmune and for the feedback.