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nservant avatar nservant commented on June 28, 2024 1

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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alongalor avatar alongalor commented on June 28, 2024

@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

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alongalor avatar alongalor commented on June 28, 2024

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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alongalor avatar alongalor commented on June 28, 2024

Absolutely agreed @nservant! This should be fixed asap.

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