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#!/bin/bash -ve
if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
gunzip -c reads.right.fq.gz > reads.right.fq
fi
if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
gunzip -c reads.left.fq.gz > reads.left.fq
fi
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
CPU=$(nproc || sysctl -n hw.physicalcpu)
${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \
--left reads.left.fq \
--right reads.right.fq \
--SS_lib_type RF \
--CPU ${CPU}\
--output trinity_with_workdir \
--workdir /tmp/trinity.workdir.$$ --full_cleanup
exit 0
|
