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...

&
(executable=run_megahit.sh)
(jobname=megahit-test)
(stdout=std.out)
(stderr=std.err)
(gmlog=gridlog_1)
(walltime=4h)
(memory=16000)
(runtimeenvironment="APPS/BIO/BIOCONDA")
(cpount=8)
(inputfiles=
( "seq_R1.fastq.gz" "seq_R1.fastq.gz" )
( "seq_R2.fastq.gz" "seq_R2.fastq.gz" )
( "seq_merged.fastq.gz" "seq_merged.fastq.gz" )
)
(outputfiles=
   ( "outputmegahit_results.tartgz" "outputmegahit_results.tartgz" )
)

 

The command script must contain the Conda installation commands. In the case of Bioconda based installations, you must first define the repository channels used by bioconda

...

#run the command
megahit -1 seq_R1.fastq.gz -2 seq_R2.fastq.gz -r seq_merged.fastq.gz -t 8 -o sample1megahit_trimresults
#pack and compress the results
tar zcvf sample1megahit_trimresults.tgz sample1megahit_trimresults

exit