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geronimp / enrichM

Toolbox for comparative genomics of MAGs
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Error when downloading database #88

Closed liangjinsong closed 4 years ago

liangjinsong commented 5 years ago

First I installed enrichM via conda following the steps below. conda create -n enrichm_0.5.0 python=3 conda activate enrichm_0.5.0 conda install -c bioconda mcl R hmmer diamond prodigal parallel openmp mmseqs2 moreutils conda install -c geronimp enrichm R install.packages('gridExtra') install.packages('optparse') q()

After the installation steps above, I downloaded the database using "enrichm data" command, then a error happened, which was showed below. Can you help to solve the problem? Thank you!

(enrichm_0.5.0) jinsong@server:/data/liangjinsong/N_update/single_group_assembly_bin/5_N_genes_usearch$ enrichm data Traceback (most recent call last): File "/data/software/miniconda3/envs/enrichm_0.5.0/bin/enrichm", line 357, in r.main(args, sys.argv) File "/data/software/miniconda3/envs/enrichm_0.5.0/lib/python3.7/site-packages/enrichm/run.py", line 283, in main self._check_general(args) File "/data/software/miniconda3/envs/enrichm_0.5.0/lib/python3.7/site-packages/enrichm/run.py", line 116, in _check_general raise Exception('The following dependencies need to be installed to run enrichm:\n%s' % (dependency_string)) Exception: The following dependencies need to be installed to run enrichm: seqmagick https://fhcrc.github.io/seqmagick

liangjinsong commented 5 years ago

Installing 'seqmagick' using 'conda install -c bioconda seqmagick' command fixed the error.