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License: Other
An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data
License: Other
Hi there,
It seems that there is an issue with the PATH
variable within deFuse.
I set up a conda environment, but deFuse does not find the tools ...
conda activate defuse-env
bowtie --help
Usage:
bowtie [options]* <ebwt> {-1 <m1> -2 <m2> | --12 <r> | --interleaved <i> | <s>} [<hit>]
<m1> Comma-separated list of files containing upstream mates (or the
(...)
defuse_run.pl -d defuse_lib_0.6.0 \
-1 SRR1106775-1M_1.fastq.gz -2 SRR1106775-1M_2.fastq.gz \
-p 8 \
-o ./ \
-r ./SRR1106775_1_defuse_results.tsv \
-a ./SRR1106775_1_defuse_results_cl.tsv \
-b ./SRR1106775_1_defuse_results_fil.tsv
(...)
Job output:
Running on shbli022
log/reads.split.000.1.sh: line 6: bowtie: command not found
In theory, if the main script is using the bin path in the config, ie. just bowtie
, it should work.
Did I miss something ?
Thanks for your help
Nicolas
Are there plans to include nonhuman species? Is there a suggestion for building the resources required to do so?
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