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langmead-lab / monorail-external

examples to run monorail externally
MIT License
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Unify Conda Environment Error #26

Closed paulranum11 closed 1 year ago

paulranum11 commented 1 year ago

I successfully ran monorail-pump through singularity but upon trying "Unify" with the following command I have encountered an error.

Command: 

/bin/bash /drive_2TB/monorail/monorail-external/singularity/run_recount_unify.sh \
        /drive_2TB/monorail/monorail-external/recount-rs5_1.0.8.sif \
        hg38 \
        /drive_2TB/monorail/monorail-external/ \
        /drive_2TB/monorail/monorail-external/ \
        /drive_2TB/monorail/monorail-external/output \
        /drive_2TB/monorail/monorail-external/sample_metadata.tsv \
        8 \
        myProjABC:100

Error: 

+++ /opt/conda/bin/conda shell.posix activate recount-unify
Could not find conda environment: recount-unify
You can list all discoverable environments with `conda info --envs`.

Question: Is the environment for Unify housed within the "recount-rs5_1.0.8.sif" file that worked for monorail pump? Or is there a different .sif environment file required for monorail unify? If "recount-rs5_1.0.8.sif" is the correct environment for monorail unify then it appears there may be some issue with the container? Any advice or suggestions would be much appreciated!

paulranum11 commented 1 year ago

Solved, my mistake, the second environment is clearly specified. For those with a similar problem it must be downloaded with singularity pull docker://quay.io/broadsword/recount-unify:1.1.1