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  • Conda/Bioconda in FGCI

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( "seq_R1.fastq.gz" "seq_R1.fastq.gz" )
( "seq_R2.fastq.gz" "seq_R2.fastq.gz" )
( "seq_merged.fastq.gz" "seq_merged.fastq.gz" )
   ( "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