#!/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 ##
#######################################################


${TRINITY_HOME}/Trinity \
    --seqType fq \
    --max_memory 2G \
    --left reads.left.fq \
    --right reads.right.fq \
    --SS_lib_type RF \
    --CPU 4 \
    --no_normalize_reads \
    --trimmomatic \
    --output __test_trinity_with_trimmomatic

##### Done Running Trinity #####

