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
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