The defuse's discuss from amcpherson

defuse's Issues

Nonhuman species

Are there plans to include nonhuman species? Is there a suggestion for building the resources required to do so?

conda and PATH

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

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