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#!/bin/bash -ve
CPU=$(nproc || sysctl -n hw.physicalcpu)
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
if [ -z ${TRINITY_HOME} ]; then
echo "Must set env var TRINITY_HOME"
exit 1
fi
${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \
--left reads.left.fq.gz \
--right reads.right.fq.gz \
--SS_lib_type RF \
--CPU ${CPU} --output trinity_out_dir_SR --NO_PARALLEL_IWORM --SUPER_READS --no_cleanup
##### Done Running Trinity #####
if [ $* ]; then
# check full-length reconstruction stats:
${TRINITY_HOME}/util/misc/illustrate_ref_comparison.pl __indiv_ex_sample_derived/refSeqs.fa trinity_out_dir_SR/Trinity.fasta 90
./test_FL.sh --query trinity_out_dir_SR/Trinity.fasta --target __indiv_ex_sample_derived/refSeqs.fa --no_reuse
fi
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