jiarong
commented
2 years ago Hi, I just tested the conda install and database setup and it worked on my server.. What's your linux distribution? (cat /etc/*release).
An alternative is to use the singlularity image: https://github.com/jiarong/VirSorter2#option-3
WEIdlam
Dear jiarong, I'm installing virsoter 2.2.3 and stucked in an error when running virsorter setup -d db -j 4. I have tried to reinstall it according to the requirements, but the same mistakes still occur. this seems to be a problem with perl. The command and error is: virsorter setup -d db -j 4 [2022-01-28 13:16 INFO] VirSorter 2.2.3 [2022-01-28 13:16 INFO] /home/pc/miniconda3/envs/vs2/bin/virsorter setup -d db -j 4 [2022-01-28 13:16 INFO] Setting up VirSorter2 database; this might take ~10 mins and only needs to be done once. [2022-01-28 13:16 INFO] saving /media/pc/0A9AD66165F33762/HB/virus_software/VirSorter2/db as DBDIR to config file /media/pc/0A9AD66165F33762/HB/virus_software/VirSorter2/virsorter/template-config.yaml [2022-01-28 13:17 ERROR] CreateCondaEnvironmentException: Could not create conda environment from /media/pc/0A9AD66165F33762/HB/virus_software/VirSorter2/virsorter/rules/../envs/vs2.yaml: Package Version Build Channel Size ─────────────────────────────────────────────────────────────────────────────────────────── Install: ───────────────────────────────────────────────────────────────────────────────────────────
zstd 1.5.2 ha95c52a_0 conda-forge/linux-64 Cached
Summary:
Install: 93 packages
Total download: 0 B
───────────────────────────────────────────────────────────────────────────────────────────
Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done ERROR conda.core.link:_execute(699): An error occurred while installing package 'conda-forge::perl-5.32.1-1_h7f98852_perl5'. Rolling back transaction: ...working... done
[Errno 22] Invalid argument: '/media/pc/0A9AD66165F33762/HB/virus_software/VirSorter2/db/conda_envs/2c70b779/man/man3/App::Cpan.3' ()
File "/home/pc/miniconda3/envs/vs2/lib/python3.8/site-packages/snakemake/deployment/conda.py", line 350, in create [2022-01-28 13:17 INFO] First attempt failed; trying the second time.
Thanks!