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#!/bin/bash
if [ ! -e Trinity.fasta ]; then
gunzip -c Trinity.fasta.gz > Trinity.fasta
gunzip -c genome_alignments.gmap.gff3.gz > genome_alignments.gmap.gff3
fi
docker run --rm -v `pwd`:/data trinityrnaseq/transdecoder:latest TransDecoder.LongOrfs -t /data/Trinity.fasta -O /data
docker run --rm -v `pwd`:/data trinityrnaseq/transdecoder:latest TransDecoder.Predict -t /data/Trinity.fasta -O /data
# gmap was used to align the Trinity.fasta transcripts to the genome,
# using the gmap '-f 3' output formatting parameter, generating file 'genome_alignments.gmap.gff3'
docker run --rm -v `pwd`:/data trinityrnaseq/transdecoder:latest bash -c "/usr/local/bin/util/cdna_alignment_orf_to_genome_orf.pl /data/Trinity.fasta.transdecoder.gff3 /data/genome_alignments.gmap.gff3 /data/Trinity.fasta > /data/Trinity.fasta.transdecoder.genome.gff3"
docker run --rm -v `pwd`:/data trinityrnaseq/transdecoder:latest /usr/local/bin/util/fasta_prot_checker.pl /data/Trinity.fasta.transdecoder.pep
exit 0
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