Author: Michael R. Crusoe <crusoe@ucdavis.edu>
Description: add #! lines as needed
--- trinityrnaseq.orig/sample_data/__regression_tests/test_GraphFromFasta/runMe.sh
+++ trinityrnaseq/sample_data/__regression_tests/test_GraphFromFasta/runMe.sh
@@ -1 +1,2 @@
+#!/bin/sh
 ../../../Chrysalis/GraphFromFasta -i inchworm.K25.L25.fa -r both.fa -min_contig_length 100 -min_glue 0 -glue_factor 0 -min_iso_ratio 0 -t 4 -k 24 -kk 48
--- trinityrnaseq.orig/sample_data/test_GOSeq_trinotate_pipe/Spombe/runMe.sh
+++ trinityrnaseq/sample_data/test_GOSeq_trinotate_pipe/Spombe/runMe.sh
@@ -1,3 +1,4 @@
+#!/bin/sh
 ../../../Analysis/DifferentialExpression/run_GOseq.pl --factor_labeling hs_induced_vs_log.factors --GO_assignments Trinotate_report.xls.trans.gene_ontology --lengths Trinity.seq_lengths
 
 ../../../Analysis/DifferentialExpression/run_GOseq.pl --factor_labeling ds_induced_vs_log.factors --GO_assignments Trinotate_report.xls.trans.gene_ontology --lengths Trinity.seq_lengths
--- trinityrnaseq.orig/sample_data/test_Inchworm/runMe_MPI.sh
+++ trinityrnaseq/sample_data/test_Inchworm/runMe_MPI.sh
@@ -1,3 +1,4 @@
+#!/bin/sh
 if [ ! -e jellyfish.kmers.fa ]; then
     gunzip -c jellyfish.kmers.fa.gz > jellyfish.kmers.fa
 fi
--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/align_reads_via_bowtie.sh
+++ trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/align_reads_via_bowtie.sh
@@ -1 +1,2 @@
-/home/unix/bhaas/SVN/trinityrnaseq/trunk/util/bowtie_PE_separate_then_join.pl --seqType fq --left ../reads.left.fq --right ../reads.right.fq --target refSeqs.fa --aligner bowtie -- -p 4 --all --best --strata -m 300
+#!/bin/bash
+/usr/lib/trinityrnaseq/util/bowtie_PE_separate_then_join.pl --seqType fq --left ../reads.left.fq --right ../reads.right.fq --target refSeqs.fa --aligner bowtie -- -p 4 --all --best --strata -m 300
--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.clean.sh
+++ trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.clean.sh
@@ -1 +1,2 @@
+#!/bin/sh
 ../../../../Trinity.pl --seqType fq --left clean.left.fq --right clean.right.fq --seqType fq --JM 1G --bfly_opts "-V 15 --stderr "
--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.sh
+++ trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.sh
@@ -1 +1,2 @@
+#!/bin/sh
 ../../../../Trinity.pl --seqType fq --left ex5.reads.left.fq --right ex5.reads.right.fq --seqType fq --JM 1G --bfly_opts "-V 15 --stderr"
--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/runMe.sh
+++ trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/runMe.sh
@@ -1,2 +1,3 @@
+#!/bin/sh
 ../../Trinity.pl --seqType fq --left ex9.reads.left.fq --right ex9.reads.right.fq --SS_lib_type RF --bfly_opts "--edge-thr=0.05 --stderr -V 18" --run_butterfly  --output trinity_outdir

