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bxlab / metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
MIT License
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additional installation step question #11

Open karoraw1 opened 6 years ago

karoraw1 commented 6 years ago

I did a fresh install of the newly named conda package into a newly created conda environment.

After installation, I exited my ssh session and then re-entered. I copied my copy of the configuration file into the new conda environment. I tried to test the installation and got the following error:

(metawrap2-env) [karoraw1@jhu.edu@bigmem0009 Scripts]$ which config-metawrap
~/scratch/miniconda2/envs/metawrap2-env/bin/config-metawrap
(metawrap2-env) [karoraw1@jhu.edu@bigmem0009 Scripts]$ metaWRAP read_qc -h
/home-3/karoraw1@jhu.edu/scratch/miniconda2/envs/metawrap2-env/bin/metaWRAP: line 33: config-metawrap: No such file or directory
/read_qc.sh -h
/home-3/karoraw1@jhu.edu/scratch/miniconda2/envs/metawrap2-env/bin/metaWRAP: line 53: /read_qc.sh: No such file or directory

I got this error the first time I installed metawrap and got around it by adding the ~/scratch/miniconda2/envs/metawrap2-env/bin directory & metawrap-modules subdirectory to $PATH.

I think this is not an ideal solution and was wondering if you had any better ideas? Otherwise, if this step is required for installation, you might want to include it in the installation instructions.

ursky commented 6 years ago

I am unable to replicate this on any system I tried. This appears to be a environment-specific issue, but thank you for posting your solution. I will contact you privately to try to resolve this.