Repository 'bowtie2'
hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/bowtie2

Changeset 0:96d2e31a3938 (2014-01-27)
Next changeset 1:a54de7e658f7 (2014-03-05)
Commit message:
Imported from capsule None
added:
bowtie2_wrapper.xml
test-data/bowtie2/phix_genome.fasta
test-data/bowtie2/phix_mapped.bam
test-data/bowtie2/phix_reads.fastq
tool-data/bowtie2_indices.loc.sample
tool_data_table_conf.xml.sample
tool_dependencies.xml
b
diff -r 000000000000 -r 96d2e31a3938 bowtie2_wrapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bowtie2_wrapper.xml Mon Jan 27 09:25:15 2014 -0500
[
b'@@ -0,0 +1,383 @@\n+<tool id="bowtie2" name="Bowtie2" version="0.2">\n+    <!-- Wrapper compatible with Bowtie version 2.0.0 -->\n+    <description>is a short-read aligner</description>\n+    <version_command>bowtie2 --version</version_command>\n+    <requirements>\n+        <requirement type="package" version="2.1.0">bowtie2</requirement>\n+        <requirement type="package" version="0.1.18">samtools</requirement>\n+    </requirements>\n+    \n+    <command>\n+        ## prepare bowtie2 index\n+        #set index_path = \'\'\n+        #if str($reference_genome.source) == "history":\n+            bowtie2-build "$reference_genome.own_file" genome; ln -s "$reference_genome.own_file" genome.fa;\n+            #set index_path = \'genome\'\n+        #else:\n+            #set index_path = $reference_genome.index.fields.path\n+        #end if\n+        \n+        ## execute bowtie2\n+        bowtie2\n+        \n+        ## number of threads\n+        -p \\${GALAXY_SLOTS:-4}\n+\n+        ## index file path\n+        -x $index_path\n+        \n+        ## check for single/pair-end\n+        #if str( $library.type ) == "single"\n+            ## prepare inputs\n+            -U $library.input_1\n+        \n+            #if $output_unaligned_reads_l\n+                --un $output_unaligned_reads_l\n+            #end if\n+        #else\n+            ## prepare inputs\n+            -1 $library.input_1\n+            -2 $library.input_2\n+            -I $library.min_insert\n+            -X $library.max_insert\n+\n+            #if $output_unaligned_reads_l\n+                --un-conc $output_unaligned_reads_l\n+            #end if\n+        #end if\n+        \n+        ## configure settings\n+        #if str($params.full) == "yes":\n+            ## add alignment type\n+            $params.align_type\n+\n+            ## add performance\n+            $params.performance\n+        \n+            ## add time flag\n+            $params.time\n+        \n+            ## add nofw/norc\n+            $params.nofw_norc\n+\n+            ## set gbar\n+            --gbar $params.gbar\n+        \n+            ## check skip\n+            #if str($params.skip) != "0":\n+                -s $params.skip\n+            #end if\n+\n+            ## check upto\n+            #if str($params.upto) != "0":\n+                -u $params.upto\n+            #end if\n+        \n+            ## check trim5\n+            #if str($params.trim5) != "0":\n+                -5 $params.trim5\n+            #end if\n+        \n+            ## check trim3\n+            #if str($params.trim3) != "0":\n+                -3 $params.trim3\n+            #end if\n+        #end if\n+        \n+        ## read group information\n+        #if str($read_group.selection) == "yes":\n+            #if $read_group.rgid and $read_group.rglb and $read_group.rgpl and $read_group.rgsm:\n+                --rg-id "$read_group.rgid"\n+                --rg "LB:$read_group.rglb"\n+                --rg "PL:$read_group.rgpl"\n+                --rg "SM:$read_group.rgsm"\n+            #end if\n+        #end if\n+        \n+        ## view/sort and output file\n+        | samtools view -Su - | samtools sort -o - - > $output\n+        \n+        ## rename unaligned sequence files\n+        #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:\n+            #set left  = str($output_unaligned_reads_l).replace( \'.dat\', \'.1.dat\' )\n+            #set right = str($output_unaligned_reads_l).replace( \'.dat\', \'.2.dat\' )\n+        \n+            ; mv $left $output_unaligned_reads_l;\n+            mv $right $output_unaligned_reads_r\n+        #end if\n+    </command>\n+    \n+    <!-- basic error handling -->\n+    <stdio>\n+        <exit_code range="1:" level="fatal" description="Tool exception" />\n+    </stdio>\n+    \n+    <inputs>\n+        <!-- single/paired -->\n+        <conditional name="library">\n+            <param name="type" type="select" label="Is this library mate-paired?">\n+              <option value="single">Single-end</option>\n+              <option value="paired">Paired-end</option>\n+      '..b'ment if doing so maximizes the alignment score.\n+\n+End-to-end alignment example::\n+\n+  Read       GACTGGGCGATCTCGACTTCG\n+             |||||  ||||||||||||||\n+  Reference  GACTG--CGATCTCGACATCG\n+\n+Local alignment example::\n+\n+  Read       ACGGTTGCGTTAA-TCCGCCACG\n+                 ||||||||| ||||||\n+  Reference  TAACTTGCGTTAAATCCGCCTGG\n+\n+*-s/--skip (default: 0)*\n+\n+Skip (i.e. do not align) the first n-reads or pairs in the input.\n+\n+*-u/--qupto (default: no limit)*\n+\n+Align the first n-reads or read pairs from the input (after the -s/--skip reads or pairs have been skipped), then stop.\n+\n+*-5/--trim5 (default: 0)*\n+\n+Trim n-bases from 5\' (left) end of each read before alignment.\n+\n+*-3/--trim3 (default: 0)*\n+\n+Trim n-bases from 3\' (right) end of each read before alignment.\n+\n+*--nofw/--norc (default: both strands enabled)*\n+\n+If --nofw is specified, Bowtie 2 will not attempt to align unpaired reads to the forward (Watson) reference strand. If --norc is specified, bowtie2 will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes Bowtie 2 to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default: both strands enabled.\n+\n+*--gbar (default: 4)*\n+\n+Disallow gaps within n-positions of the beginning or end of the read.\n+\n+------\n+\n+**Paired-end options**\n+\n+*-I/--minins (default: 0)*\n+\n+The minimum fragment length for valid paired-end alignments. E.g. if -I 60 is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as -X is also satisfied). A 19-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -I constraint is applied with respect to the untrimmed mates.\n+\n+The larger the difference between -I and -X, the slower Bowtie 2 will run. This is because larger differences bewteen -I and -X require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient.\n+\n+*-X/--maxins (default: 0)*\n+\n+The maximum fragment length for valid paired-end alignments. E.g. if -X 100 is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied). A 61-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -X constraint is applied with respect to the untrimmed mates, not the trimmed mates.\n+\n+The larger the difference between -I and -X, the slower Bowtie 2 will run. This is because larger differences bewteen -I and -X require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient.\n+\n+------\n+\n+**SAM options**\n+\n+*--rg-id [text]*\n+\n+Set the read group ID to [text]. This causes the SAM @RG header line to be printed, with [text] as the value associated with the ID: tag. It also causes the RG:Z: extra field to be attached to each SAM output record, with value set to [text].\n+\n+*--rg [text]*\n+\n+Add [text] as a field on the @RG header line. Note: in order for the @RG line to appear, --rg-id must also be specified. This is because the ID tag is required by the SAM Spec. Specify --rg multiple times to set multiple fields. See the SAM Spec for details about what fields are legal.\n+\n+------\n+\n+**Output options**\n+\n+*--un/--un-conc*\n+\n+Write reads that fail to align concordantly to file(s). These reads correspond to the SAM records.\n+\n+*-t/--time (default: off)*\n+\n+Print the wall-clock time required to load the index files and align the reads. This is printed to the "standard error" ("stderr") filehandle.\n+\n+    </help>\n+</tool>\n'
b
diff -r 000000000000 -r 96d2e31a3938 test-data/bowtie2/phix_genome.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bowtie2/phix_genome.fasta Mon Jan 27 09:25:15 2014 -0500
b
@@ -0,0 +1,78 @@
+>gi|9626372|ref|NC_001422.1| Enterobacteria phage phiX174, complete genome
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
\ No newline at end of file
b
diff -r 000000000000 -r 96d2e31a3938 test-data/bowtie2/phix_mapped.bam
b
Binary file test-data/bowtie2/phix_mapped.bam has changed
b
diff -r 000000000000 -r 96d2e31a3938 test-data/bowtie2/phix_reads.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bowtie2/phix_reads.fastq Mon Jan 27 09:25:15 2014 -0500
[
b'@@ -0,0 +1,260 @@\n+@HWI-EAS210R_0001:4:10:890:1882#0/1\n+AATCTCATCTCTCTTTTTGCGTTCTGCTTCAATATCTG\n++HWI-EAS210R_0001:4:10:890:1882#0/1\n+fcceeggggggggggggffghggggggggggggggggg\n+@HWI-EAS210R_0001:4:10:890:1010#0/1\n+GTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGA\n++HWI-EAS210R_0001:4:10:890:1010#0/1\n+gggggggggggggghgggggggggfggggggggggggg\n+@HWI-EAS210R_0001:4:10:890:1780#0/1\n+GAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTAT\n++HWI-EAS210R_0001:4:10:890:1780#0/1\n+ggfhggggggggggggggggghgggggfggggggdggg\n+@HWI-EAS210R_0001:4:10:890:1348#0/1\n+TTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT\n++HWI-EAS210R_0001:4:10:890:1348#0/1\n+ggggggggggggggggggggggggghfggeggggggdg\n+@HWI-EAS210R_0001:4:10:890:1707#0/1\n+AAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCC\n++HWI-EAS210R_0001:4:10:890:1707#0/1\n+gfgfgfgggggggfggeggggffgcgggdfggfggdgg\n+@HWI-EAS210R_0001:4:10:890:1527#0/1\n+CGTACTTATTCGCCACCATGATTATGACCAGTGTTTCC\n++HWI-EAS210R_0001:4:10:890:1527#0/1\n+gggggggggggggggggggggggggggggggggggggg\n+@HWI-EAS210R_0001:4:10:890:781#0/1\n+CGGAAAACGAACAAGCGCAAGAGTAAACATAGTGCCAT\n++HWI-EAS210R_0001:4:10:890:781#0/1\n+gggggggggggggggggggggggggggggggghggggg\n+@HWI-EAS210R_0001:4:10:890:568#0/1\n+GTTTATCGCAATCTGCCGACCACTCGCGATTCAATCAT\n++HWI-EAS210R_0001:4:10:890:568#0/1\n+gggggggfgggggggggggggggggggggggggggggg\n+@HWI-EAS210R_0001:4:10:890:1365#0/1\n+CCAACATAAACATTATTGCCCGGCGTACGAGGAAGGAC\n++HWI-EAS210R_0001:4:10:890:1365#0/1\n+eggggdggfghggggggggghgfgfegghfggfgggge\n+@HWI-EAS210R_0001:4:10:890:161#0/1\n+GTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCT\n++HWI-EAS210R_0001:4:10:890:161#0/1\n+ggggfg_gggfegggfgeggaefefdbfddeedgcgg`\n+@HWI-EAS210R_0001:4:10:890:1920#0/1\n+TTTATCAATACCATGAAAAATATCAACCACACCAGAAG\n++HWI-EAS210R_0001:4:10:890:1920#0/1\n+gggggggggggggggggggggffggggggggggggggg\n+@HWI-EAS210R_0001:4:10:890:61#0/1\n+GTCGCGTCGTAACCCAGCTTGGTAAGTTGGATTAAGCA\n++HWI-EAS210R_0001:4:10:890:61#0/1\n+eede[egfggfggggggggggggegggggfgggggggg\n+@HWI-EAS210R_0001:4:10:890:1284#0/1\n+AAGCGCAAGAGTAAACATAGTGCCATGCTCAGGAACAA\n++HWI-EAS210R_0001:4:10:890:1284#0/1\n+gggggggggggggggggggggggggggggggggggggg\n+@HWI-EAS210R_0001:4:10:890:208#0/1\n+CAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCC\n++HWI-EAS210R_0001:4:10:890:208#0/1\n+gggeggggggggggggggggggggggggggggddgggg\n+@HWI-EAS210R_0001:4:10:890:859#0/1\n+CAATAGATGTGGTAGAAGTCGTCATTTGGCGAGAAAGC\n++HWI-EAS210R_0001:4:10:890:859#0/1\n+ggggcgggggggggggdgfggggggggfggggghgggh\n+@HWI-EAS210R_0001:4:10:890:1947#0/1\n+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGAT\n++HWI-EAS210R_0001:4:10:890:1947#0/1\n+ggggggggggggggggggeggggggggggggfgfgggg\n+@HWI-EAS210R_0001:4:10:890:416#0/1\n+AATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTG\n++HWI-EAS210R_0001:4:10:890:416#0/1\n+eggggggggggdcgggggfggfgggggfcgfggggggg\n+@HWI-EAS210R_0001:4:10:890:654#0/1\n+GCAGCAAGGTCCATATCTGACTTTTTGTTAACGTATTT\n++HWI-EAS210R_0001:4:10:890:654#0/1\n+ggggghggggghggggghgfggggfgdfffgggggggg\n+@HWI-EAS210R_0001:4:10:890:269#0/1\n+CTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGG\n++HWI-EAS210R_0001:4:10:890:269#0/1\n+eecaadggggggggggggggggdgg\\ffffgggggggg\n+@HWI-EAS210R_0001:4:10:890:657#0/1\n+TACCAGCTTTAGCCATAGCACCAGAAACAAAACTAGGG\n++HWI-EAS210R_0001:4:10:890:657#0/1\n+ggggghggggffgggfggggggfggfggggfffgfggg\n+@HWI-EAS210R_0001:4:10:890:1449#0/1\n+TTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTA\n++HWI-EAS210R_0001:4:10:890:1449#0/1\n+ggggggggggggggggfgggghgggggggggggghhfh\n+@HWI-EAS210R_0001:4:10:890:305#0/1\n+CACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATA\n++HWI-EAS210R_0001:4:10:890:305#0/1\n+gggegggfgggfggggggdgggdggfgffggggggfhg\n+@HWI-EAS210R_0001:4:10:890:1190#0/1\n+AATAAGCAATGACGGCAGCAATAAACTCAACAGGAGCA\n++HWI-EAS210R_0001:4:10:890:1190#0/1\n+bbecb_gggggggggggggggggggcgggfVgggeggg\n+@HWI-EAS210R_0001:4:10:890:1586#0/1\n+ATTAGCTGTACCATACTCAGGCACACAAAAATACTGAT\n++HWI-EAS210R_0001:4:10:890:1586#0/1\n+eggWgaa^O[\\`[\\_]J_^][`W`\\]K^BBBBBBBBBB\n+@HWI-EAS210R_0001:4:10:890:617#0/1\n+AAACGCAAGCCTCAACGCAGCGACGAGCACGAGAGCGG\n++HWI-EAS210R_0001:4:10:890:617#0/1\n+gggggggggggggggggggggggggggggggggggggg\n+@HWI-EAS210R_0001:4:10:890:1562#0/1\n+GTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATC\n++HWI-EAS210R_0001:4:10:890:1562#0/1\n+hggffggggdgggggaageef`Waegggbgggcgddgg\n+@H'..b'ggggggggggggggggggggggggfggggg\n+@HWI-EAS210R_0001:4:10:890:287#0/1\n+GTATCCAACCTGCAGAGTTTTATCGCTTCCATGACGCA\n++HWI-EAS210R_0001:4:10:890:287#0/1\n+ggggggfcggggg^fbe``egggggggdgg`dddfggg\n+@HWI-EAS210R_0001:4:10:890:335#0/1\n+AAGAGGTTTTACCTCCAAATGAAGAAATAACATCATGG\n++HWI-EAS210R_0001:4:10:890:335#0/1\n+`^_``Q[cccggfgggggggbddg\\dXdbegggddfg`\n+@HWI-EAS210R_0001:4:10:891:149#0/1\n+TTTAAGAGCCTCGATACGCTCAAAGTCAAAATAATCAG\n++HWI-EAS210R_0001:4:10:891:149#0/1\n+ggggghgggggghggggggggggggfgggggggffggg\n+@HWI-EAS210R_0001:4:10:891:445#0/1\n+ATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACT\n++HWI-EAS210R_0001:4:10:891:445#0/1\n+gggggggddggggggggggggggggggggggggggggg\n+@HWI-EAS210R_0001:4:10:891:1476#0/1\n+GGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCG\n++HWI-EAS210R_0001:4:10:891:1476#0/1\n+ggegggffghhggfhggfgeggffgggffggagfggfg\n+@HWI-EAS210R_0001:4:10:891:323#0/1\n+TGTAAAACAGGTGCCGAAGAAGCTGGAGTAACAGAAGT\n++HWI-EAS210R_0001:4:10:891:323#0/1\n+gggcgfefghgggghgfgfgggggggggegaaeeagge\n+@HWI-EAS210R_0001:4:10:891:69#0/1\n+CTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTAC\n++HWI-EAS210R_0001:4:10:891:69#0/1\n+gggefgggfgafP_Vdbacbgegebd`fbaeggaggQd\n+@HWI-EAS210R_0001:4:10:891:1379#0/1\n+GACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAAT\n++HWI-EAS210R_0001:4:10:891:1379#0/1\n+gggggggggggggggggggggggggggggfgefggggg\n+@HWI-EAS210R_0001:4:10:891:608#0/1\n+CTTATGCTAATTTGCATACTGACCAAGAACGTGATTAC\n++HWI-EAS210R_0001:4:10:891:608#0/1\n+ggggggggggggggggggggggggfggggggggggggg\n+@HWI-EAS210R_0001:4:10:891:1831#0/1\n+GTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTA\n++HWI-EAS210R_0001:4:10:891:1831#0/1\n+ggggggggggggggggghggggggggghgggggfgggg\n+@HWI-EAS210R_0001:4:10:891:412#0/1\n+TAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACG\n++HWI-EAS210R_0001:4:10:891:412#0/1\n+gggggggggggggggggggggggggggggggggggggg\n+@HWI-EAS210R_0001:4:10:891:346#0/1\n+AATTCATCCATTAACTTCTCATCAACATATACAAACTC\n++HWI-EAS210R_0001:4:10:891:346#0/1\n+^W][_b^be_cRgaggdgdgbL_^_\\ZN\\R]]`W]cYe\n+@HWI-EAS210R_0001:4:10:891:174#0/1\n+AGTGGAGGCCTCCAGCAATCTTGAACACTCATCCTTAA\n++HWI-EAS210R_0001:4:10:891:174#0/1\n+ggggggggggggggggggggggcgggggfgggghghcg\n+@HWI-EAS210R_0001:4:10:891:1415#0/1\n+ACCAACCATCAGCATGAGCCTGTCGCATTGCATTCATC\n++HWI-EAS210R_0001:4:10:891:1415#0/1\n+gggggggggggdghgggggggggggggggggggggggg\n+@HWI-EAS210R_0001:4:10:891:705#0/1\n+TTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTC\n++HWI-EAS210R_0001:4:10:891:705#0/1\n+gfgggggggggfgggggggggggfgddgggggggeggg\n+@HWI-EAS210R_0001:4:10:891:1398#0/1\n+GCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAA\n++HWI-EAS210R_0001:4:10:891:1398#0/1\n+ebehggdhdfgffdda`e\\ecgfggedgegeggdfdfg\n+@HWI-EAS210R_0001:4:10:891:971#0/1\n+TAGCTTTAAGCGGCTCACCTTTAGCATCAACAGGCCAC\n++HWI-EAS210R_0001:4:10:891:971#0/1\n+ggfgggghggggggfggfgghggfggggfghggffghg\n+@HWI-EAS210R_0001:4:10:891:627#0/1\n+GTCGCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAA\n++HWI-EAS210R_0001:4:10:891:627#0/1\n+dfdffaeaaagggg[bgggghgghgggfgg\\efefggd\n+@HWI-EAS210R_0001:4:10:891:1822#0/1\n+GAGTAGTTGAAATGGTAATAAGACGACCAATCTGACCA\n++HWI-EAS210R_0001:4:10:891:1822#0/1\n+gggeggfggegggggdggggghgfgedgggggcfgdcg\n+@HWI-EAS210R_0001:4:10:891:1103#0/1\n+AAGGGTAATAAGAACGAACCATAAAAAAGCCTCCAAGA\n++HWI-EAS210R_0001:4:10:891:1103#0/1\n+ggeggfggggggggghggggggggggfffgdggggggb\n+@HWI-EAS210R_0001:4:10:891:586#0/1\n+TATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC\n++HWI-EAS210R_0001:4:10:891:586#0/1\n+ggggggggggggegfgggfcgggggffggggggggggg\n+@HWI-EAS210R_0001:4:10:891:1620#0/1\n+TTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCT\n++HWI-EAS210R_0001:4:10:891:1620#0/1\n+gggggfggggghgggggghcgggdgggegggefgfT``\n+@HWI-EAS210R_0001:4:10:891:42#0/1\n+CTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTA\n++HWI-EAS210R_0001:4:10:891:42#0/1\n+ggefggggggfggggfaf_fggggdfggggfaYbfd]b\n+@HWI-EAS210R_0001:4:10:891:1609#0/1\n+GCCATAGCACCAGAAACAAAACTAGGGGCGGCCTCATC\n++HWI-EAS210R_0001:4:10:891:1609#0/1\n+gggghgggghfgghgggggfffggggcgggfdggfggf\n+@HWI-EAS210R_0001:4:10:891:1028#0/1\n+AATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAAT\n++HWI-EAS210R_0001:4:10:891:1028#0/1\n+gfgggggggdgbggfgegeeggggggggdggegggddg\n+@HWI-EAS210R_0001:4:10:891:902#0/1\n+ATAAACATCATAGGCAGTCGGGAGGGTAGTCGGAACCG\n++HWI-EAS210R_0001:4:10:891:902#0/1\n+ggggggfgggggggggggggggggfddggggggggggg\n'
b
diff -r 000000000000 -r 96d2e31a3938 tool-data/bowtie2_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bowtie2_indices.loc.sample Mon Jan 27 09:25:15 2014 -0500
b
@@ -0,0 +1,37 @@
+# bowtie2_indices.loc.sample
+# This is a *.loc.sample file distributed with Galaxy that enables tools
+# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2.
+# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
+# First create these data files and save them in your own data directory structure.
+# Then, create a bowtie_indices.loc file to use those indexes with tools.
+# Copy this file, save it with the same name (minus the .sample), 
+# follow the format examples, and store the result in this directory.
+# The file should include an one line entry for each index set.
+# The path points to the "basename" for the set, not a specific file.
+# It has four text columns seperated by TABS.
+#
+# <unique_build_id> <dbkey> <display_name> <file_base_path>
+#
+# So, for example, if you had hg18 indexes stored in:
+#
+#    /depot/data2/galaxy/hg19/bowtie2/
+#
+# containing hg19 genome and hg19.*.bt2 files, such as:
+#    -rw-rw-r-- 1 james   james   914M Feb 10 18:56 hg19canon.fa
+#    -rw-rw-r-- 1 james   james   914M Feb 10 18:56 hg19canon.1.bt2
+#    -rw-rw-r-- 1 james   james   683M Feb 10 18:56 hg19canon.2.bt2
+#    -rw-rw-r-- 1 james   james   3.3K Feb 10 16:54 hg19canon.3.bt2
+#    -rw-rw-r-- 1 james   james   683M Feb 10 16:54 hg19canon.4.bt2
+#    -rw-rw-r-- 1 james   james   914M Feb 10 20:45 hg19canon.rev.1.bt2
+#    -rw-rw-r-- 1 james   james   683M Feb 10 20:45 hg19canon.rev.2.bt2
+#
+# then the bowtie2_indices.loc entry could look like this:
+#
+#hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon
+#
+#More examples:
+#
+#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10
+#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3
+#
+#
b
diff -r 000000000000 -r 96d2e31a3938 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Mon Jan 27 09:25:15 2014 -0500
b
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of indexes in the Bowtie2 mapper format for TopHat2 to use -->
+    <table name="tophat2_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/bowtie2_indices.loc" />
+    </table>
+</tables>
b
diff -r 000000000000 -r 96d2e31a3938 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Jan 27 09:25:15 2014 -0500
b
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="bowtie2" version="2.1.0">
+      <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="samtools" version="0.1.18">
+      <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>