Comments (4)
Hi @alongator,
I fixed it as you did so far. But to me, this solution is a bit conterintuitive based on the 'normal' conda usage.
Best
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@nservant were you able to solve this? I am encountering the same issue: https://bitbucket.org/dranew/defuse/issues/80/defuse_create_refpl-job-command-with
from defuse.
Found a simple workaround: modify your config.txt
so that your tools have their "full path" prepended.
E.g. in config.txt
, modify the Paths to external tools
section from:
# Paths to external tools
samtools_bin = samtools
bowtie_bin = bowtie
bowtie_build_bin = bowtie-build
blat_bin = blat
fatotwobit_bin = faToTwoBit
r_bin = R
rscript_bin = Rscript
gmap_bin = gmap
gmap_build_bin = gmap_build
To:
# Paths to external tools
samtools_bin = /path/to/anaconda3/envs/defuse/bin/samtools
bowtie_bin = /path/to/anaconda3/envs/defuse/bin/bowtie
bowtie_build_bin = /path/to/anaconda3/envs/defuse/bin/bowtie-build
blat_bin = /path/to/anaconda3/envs/defuse/bin/blat
fatotwobit_bin = /path/to/anaconda3/envs/defuse/bin/faToTwoBit
r_bin = /path/to/anaconda3/envs/defuse/bin/R
rscript_bin = /path/to/anaconda3/envs/defuse/bin/Rscript
gmap_bin = /path/to/anaconda3/envs/defuse/bin/gmap
gmap_build_bin = /path/to/anaconda3/envs/defuse/bin/gmap_build
*Assuming you are using anaconda3
and have installed defuse into a virtual environment named defuse
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Absolutely agreed @nservant! This should be fixed asap.
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