# HG changeset patch
# User bitlab
# Date 1570445061 14400
# Node ID acbe7e0ef559b812490f3061ca186751cb434941
# Parent  07f4c763fcd4240e7624e5c7aaeeed1986af73f9
Fixed absolute paths

diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/bin/FragHits
Binary file gecko/bin/FragHits has changed
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/bin/combineFrags
Binary file gecko/bin/combineFrags has changed
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/bin/filterFrags
Binary file gecko/bin/filterFrags has changed
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/bin/filterHits
Binary file gecko/bin/filterHits has changed
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/bin/fragStat
Binary file gecko/bin/fragStat has changed
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/bin/frags2align.sh
--- a/gecko/bin/frags2align.sh	Tue Dec 18 07:09:25 2018 -0500
+++ b/gecko/bin/frags2align.sh	Mon Oct 07 06:44:21 2019 -0400
@@ -8,7 +8,12 @@
    exit -1
 fi
 
-MGDIR=/home/galaxy-bitlab/temp
+
+
+MYRAND=$((( RANDOM % 10000000) +1))
+MGDIR=${PWD}/${MYRAND}
+
+mkdir $MGDIR
 
 FRAGS=$1
 FASTAX=$2
@@ -42,10 +47,6 @@
 
 $BINDIR/frags2text $MGDIR/$fragsName.frags $MGDIR/$fastaXname.fasta $MGDIR/$fastaYname.fasta $MGDIR/$fastaYname.rev $MGDIR/$fastaXname.idx $MGDIR/$fastaYname.idx $MGDIR/$fastaYname.rev.idx $MGDIR/$alignName.txt
 
-rm $MGDIR/$fastaXname.idx
-rm $MGDIR/$fastaYname.idx
-rm $MGDIR/$fastaYname.rev
-rm $MGDIR/$fastaYname.rev.idx
-
 mv $MGDIR/$alignName.txt $ALIGN
 
+rm -rf $MGDIR
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/bin/frags2text
Binary file gecko/bin/frags2text has changed
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/bin/getInfo
Binary file gecko/bin/getInfo has changed
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/bin/hdStat
Binary file gecko/bin/hdStat has changed
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/bin/hits
Binary file gecko/bin/hits has changed
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/bin/hitsStat
Binary file gecko/bin/hitsStat has changed
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/bin/indexmaker
Binary file gecko/bin/indexmaker has changed
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/bin/reverseComplement
Binary file gecko/bin/reverseComplement has changed
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/bin/sortHits
Binary file gecko/bin/sortHits has changed
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/bin/sortWords
Binary file gecko/bin/sortWords has changed
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/bin/w2hd
Binary file gecko/bin/w2hd has changed
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/bin/words
Binary file gecko/bin/words has changed
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/bin/wordsStat
Binary file gecko/bin/wordsStat has changed
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/bin/workflow.sh
--- a/gecko/bin/workflow.sh	Tue Dec 18 07:09:25 2018 -0500
+++ b/gecko/bin/workflow.sh	Mon Oct 07 06:44:21 2019 -0400
@@ -10,7 +10,8 @@
    exit -1
 fi
 
-#{
+
+{
 
 
 MYRAND=$((( RANDOM % 10000000) +1))
@@ -163,3 +164,5 @@
 
 rm -r ${MGDIR}
 
+} &> /dev/null
+
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/frags2align.xml
--- a/gecko/frags2align.xml	Tue Dec 18 07:09:25 2018 -0500
+++ b/gecko/frags2align.xml	Mon Oct 07 06:44:21 2019 -0400
@@ -5,7 +5,7 @@
     <param name="fastaX" type="data" format="fasta" label="x Genome" help="Single genome file in fasta format"/>    
     <param name="fastaY" type="data" value="fasta" label="y Genome" help="Single genome file in fasta format" />
   </inputs>
-  <command>/home/galaxy-bitlab/galaxy/tools/gecko/bin/frags2align.sh $fragsFile $fastaX $fastaY $alignments </command>
+  <command> make all -C ${__tool_directory__}/src/ ; ${__tool_directory__}/bin/frags2align.sh $fragsFile $fastaX $fastaY $alignments </command>
   <outputs>
     <data name="alignments" format="txt" label="Frags to align for genomes  ${fastaX.name}_${fastaY.name}"/>
   </outputs>
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/gecko.xml
--- a/gecko/gecko.xml	Tue Dec 18 07:09:25 2018 -0500
+++ b/gecko/gecko.xml	Mon Oct 07 06:44:21 2019 -0400
@@ -1,7 +1,7 @@
 <tool id="GECKO" name="GECKO" version="1.0.1">
   <description>A pairwise genome comparison software for the detection of High-scoring Segment Pairs</description>
 
-  <command>/home/galaxy-bitlab/galaxy/tools/gecko/bin/workflow.sh $genome1 $genome2 $length $similarity $wl 1 $frags_output0 $csv_output1</command>
+  <command>make all -C ${__tool_directory__}/src ; ${__tool_directory__}/bin/workflow.sh $genome1 $genome2 $length $similarity $wl 1 $frags_output0 $csv_output1</command>
 
   <inputs>
     <param name="genome1" type="data" format="fasta" label="Sequence X" help="Query sequence file in fasta format" />
@@ -12,7 +12,7 @@
   </inputs>
 
   <outputs>
-     <data name="frags_output0" format="data" label="Frags comparison for ${genome1.name}_${genome2.name}"/>
+     <data name="frags_output0" type="data" format="frags" label="Frags comparison for ${genome1.name}_${genome2.name}"/>
      <data name="csv_output1" format="csv" label="Csv comparison for ${genome1.name}_${genome2.name}"/> 
   </outputs>
 
diff -r 07f4c763fcd4 -r acbe7e0ef559 gecko/src/reverseComplement.c
--- a/gecko/src/reverseComplement.c	Tue Dec 18 07:09:25 2018 -0500
+++ b/gecko/src/reverseComplement.c	Mon Oct 07 06:44:21 2019 -0400
@@ -15,7 +15,7 @@
 #include <inttypes.h>
 #include "commonFunctions.h"
 
-#define SEQSIZE 2000000000
+#define SEQSIZE 500000000
 #define WSIZE 32
 #define NREADS 1000000