# HG changeset patch
# User trinity_ctat
# Date 1523544774 14400
# Node ID 854531fa16459441428b84406e594d61b968b34f

Making sure tools are up to date.

diff -r 000000000000 -r 854531fa1645 ctat_gmap_fusion.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ctat_gmap_fusion.xml	Thu Apr 12 10:52:54 2018 -0400
@@ -0,0 +1,55 @@
+<tool id="ctat_gmap_fusion" name="ctat_gmap_fusion" version="1.0.0" profile="17.05">
+    <description>Fusion-finding Using De novo RNA-Seq Transcript Assemblies</description>
+    <requirements>
+        <requirement type="package" version="0.4.0">gmap-fusion</requirement>
+    </requirements>
+    <command detect_errors="default">
+      GMAP-fusion 
+      -T $assembled_trans 
+      --left_fq $left_input
+      --right_fq $right_input
+      --genome_lib_dir "${genome_ref_lib.fields.path}"
+      --output "subdir" 
+    </command>
+    <stdio>
+      <exit_code range="1:"  level="fatal"   description="Error returned from pipeline" />
+    </stdio>
+    <regex match="Must investigate error above."
+           source="stderr"
+           level="fatal"
+           description="Unknown error encountered" />
+    <inputs>
+      <param format="fasta" name="assembled_trans" type="data" label="Assembled Transcripts (ie. Trinity or DISCASM output)" help="Trinity or DISCASM generated transcript fasta"/>
+      <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help="Forward strand reads"/>
+      <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help="Reverse strand reads"/>
+      <param name="genome_ref_lib" type="select" label="Select a reference genome">
+        <options from_data_table="ctat_genome_ref_libs">
+          <filter type="sort_by" column="2" />
+          <validator type="no_options" message="No indexes are available" />
+        </options>
+      </param>
+    </inputs>
+    <outputs>
+      <data format="tabular" name="gmapfusion_candidates" label="${tool.name} on ${on_string}: GMAP-fusion candidates" from_work_dir="subdir/GMAP-fusion.final"/>
+    </outputs>
+
+    <tests>
+      <test>
+        <param name="left_input" value="GMAP/reads_1.fq.gz" />
+        <param name="right_input" value="GMAP/reads_2.fq.gz" />
+        <param name="assembled_trans" value="GMAP/transcripts.fa" />
+        <!-- FIX - now that we added the CTAT ref lib path as a parameter, how do we find it for testing?
+        <param name="genome_ref_lib.fields.path" value="?????" />
+        -->
+        <output name="gmapfusion_candidates" file="GMAP/fusion.reads_1_2.final" />
+      </test>
+    </tests>
+
+    <help>
+.. class:: infomark
+
+GMAP-fusion is a utility for identifying candidate fusion transcripts based on transcript sequences reconstructed via RNA-Seq de novo transcriptome assembly.  Please read more here_.
+
+.. _here: https://github.com/GMAP-fusion/GMAP-fusion/wiki
+    </help>
+</tool>
diff -r 000000000000 -r 854531fa1645 test-data/GMAP/fusion.reads_1_2.final
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GMAP/fusion.reads_1_2.final	Thu Apr 12 10:52:54 2018 -0400
@@ -0,0 +1,7 @@
+#fusion_name	J	S	trans_acc	trans_brkpt	geneA	chrA	coordA	geneB	chrB	coordB	junction_type
+RPS6KB1--SNF8	10	22	Locus_20_Transcript_1/1_Confidence_1.000_Length_350	156-157	RPS6KB1	chr17	57970686	SNF8	chr17	47021337	ONLY_REF_SPLICE
+ACACA--STAC2	9	22	Locus_6_Transcript_1/1_Confidence_1.000_Length_398	170-171	ACACA	chr17	35479453	STAC2	chr17	37374426	ONLY_REF_SPLICE
+VAPB--IKZF3	1	21	Locus_24_Transcript_1/1_Confidence_1.000_Length_308	168-169	VAPB	chr20	56964573	IKZF3	chr17	37934020	ONLY_REF_SPLICE
+AHCTF1--NAAA	3	8	Locus_44_Transcript_1/1_Confidence_1.000_Length_339	133-134	AHCTF1	chr1	247094880	NAAA	chr4	76846964	ONLY_REF_SPLICE
+MED1--ACSF2	4	2	Locus_51_Transcript_1/1_Confidence_1.000_Length_187	88-87	MED1	chr17	37595418	ACSF2	chr17	48548389	ONLY_REF_SPLICE
+TOB1--SYNRG	1	1	Locus_26_Transcript_1/1_Confidence_1.000_Length_201	90-91	TOB1	chr17	48943419	SYNRG	chr17	35880751	ONLY_REF_SPLICE
diff -r 000000000000 -r 854531fa1645 test-data/GMAP/reads_1.fq.gz
Binary file test-data/GMAP/reads_1.fq.gz has changed
diff -r 000000000000 -r 854531fa1645 test-data/GMAP/reads_2.fq.gz
Binary file test-data/GMAP/reads_2.fq.gz has changed
diff -r 000000000000 -r 854531fa1645 test-data/GMAP/transcripts.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GMAP/transcripts.fa	Thu Apr 12 10:52:54 2018 -0400
@@ -0,0 +1,250 @@
+>Locus_1_Transcript_1/1_Confidence_1.000_Length_106
+GCCATCTTTTACTGCTGTTGGAACACCAGCTACTGTGACTACCCCTGCCAGCAAGCCCAC
+TGGCCTGAGCACATGAAGTCCTGCACCCAGTCAGGAGAAGGAGCGC
+>Locus_2_Transcript_1/1_Confidence_1.000_Length_1407
+CCCCAACTAAATACTACCGTATGGCCCACCATAATTACCCCCATACTCCTTACACTATTC
+CTCATCACCCAACTAAAAATATTAAACACAAACTACCACCTACCTCCCTCACCAAAGCCC
+ATAAAAATAAAAAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTT
+CATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCC
+CTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGACTAATCACCACCCAACAAT
+GACTAATCAAACTAACCTCAAAACAAATGATAACCATACACAACACTAAAGGACGAACCT
+GATCTCTTATACTAGTATCCTTAATCATTTTTATTGCCACAACTAACCTCCTCGGACTCC
+TGCCTCACTCATTTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCT
+TATGAGCGGGCGCAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCCTAGCCCACT
+TCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGAAACCATCA
+GCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCC
+ACCTACTCATGCACCTAATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCT
+CTACACTTATCATCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCT
+TAATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACAACACATAAT
+GACCCACCAATCACATGCCTATCATATAGTAAAACCCAGCCCATGACCCCTAACAGGGGC
+CCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATTTCACTTCCACTCCATAAC
+GCTCCTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGGCGCGATGT
+AACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATA
+CGGGATAATCCTATTTATTACCTCAGAAATTTTTTTCTTCGCAGGGTTTTTCTGAGCCTT
+TTACCACTCCAGCCTAGCCCCTACCCCCCAATTAGGAGGGCACTGGCCCCCAACAGGCAT
+CACCCCGCTAAATCCCCTAGAAGTCCCACTCCTAAACACATCCGTATTACTCGCATCAGG
+AGTATCAATCACCTGAGCTCACCATAGTCTAATAGAAAACAACCGAAACCAAATAATTCA
+AGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTA
+CTTCGAGTCTCCCTTCACCATTTCCGA
+>Locus_3_Transcript_1/1_Confidence_1.000_Length_351
+TCGCGGGGACACCGGGGGGGCGCCGGGGGCCTCCCACTTATTCTACACCTCTCATGTCTC
+TTCACCGTGCCAGACTAGAGTCAAGCTCAACAGGGTCTTCTTTCCCCGCTGATTCCGCCA
+AGCCCGTTCCCTTGGCTGTGGTTTCGCTGGATAGTAGGTAGGGACAGTGGGAATCTCGTT
+CATCCATTCATGCGCGTCACTAATTAGATGACGAGGCATTTGGCTACCTTAAGAGAGTCA
+TAGTTACTCCCGCCGTTTACCCGCGCTTCATTGAATTTCTTCACTTTGACATTCAGAGCA
+CTGGGCAGAAATCACATCGCGTCAACACCCGCCGGAGGAGGAGACCCCATT
+>Locus_5_Transcript_1/1_Confidence_1.000_Length_226
+TCCGCAAGCCTGTGACGGTCCATTCCCGGGCTCGATGCCGGAAAAACACCTTGGCCCGCC
+GGAAGGGCAGGCACATGGGCATAGGTAAGCGGAAGGGTACAGCCAATGCCCGAATGCCAG
+AGAAGGTCACATGGATGAGGAGAATGAGGATTTTGCGCCGGCTGCTCAGAAGATACCGTG
+AATCTAAGAAGATCGATCGCCACATGTATCACAGCCTGTACCTGAA
+>Locus_6_Transcript_1/1_Confidence_1.000_Length_398
+GCTTTTTTGACTATGGATCTTTCTCAGAGATTATGCAGCCCTGGGCACAGACTGTGGTGG
+TTGGTAGAGCCAGGCTAGGAGGAATACCTGTGGGAGTTGTTGCTGTAGAAACCCGAACAG
+TAGAACTAAGTATCCCAGCTGATCCAGCAAACCTGGATTCTGAAGCCAAGCTCCAGCGAT
+TCAAGCGCTCCCTCTCCCTCAAGACCATCCTCCGAAGTAAGAGCTTGGAGAACTTCTTCC
+TTCGCTCGGGCTCTGAGCTCAAGTGCCCCACCGAGGTGCTGCTGACGCCCCCAACCCCAC
+TGCCCCCTCCCTCCCCACCACCCACAGCCTCGGACAGGGGCCTGGCTACCCCATCCCCCT
+CCCCATGCCCAGTCCCACGCCCCCTGGCAGCGCTCAAA
+>Locus_7_Transcript_1/2_Confidence_0.667_Length_226
+GCCCATCGCAGCACCAATGCCCAGGGCAGCCATTGGAAACAGAGGCGGAAATTCCTGCCC
+GATGACATTGGCCAGTCACCCATTGTCTCCATGCCGGACGGAGACAAGGTGGACCTGGAA
+GCCTTCAGCGAGTTTACCAAGATCATCACCCCGGCCATCACCCGTGTGGTGGACTTTGCC
+AAAAAACTGCCCATGTTCTCCGAGTGTGGAGAAAAGAGAGAGAAAG
+>Locus_7_Transcript_2/2_Confidence_0.667_Length_268
+GCCCATCGCAGCACCAATGCCCAGGGCAGCCATTGGAAACAGAGGCGGAAATTCCTGCCC
+GATGACATTGGCCAGTCACCCATTGTCTCCATGCCGGACGGAGACAAGGTGGACCTGGAA
+GCCTTCAGCGAGTTTACCAAGATCATCACCCCGGCCATCACCCGTGTGGTGGACTTTGCC
+AAAAAACTGCCCATGTTCTCCGAGCAATTTCGAGTGCAAGTGCCACAGTGTCAGCTAAAG
+AAACACAACTGCGGGTTTTCTGCAGAGC
+>Locus_8_Transcript_1/1_Confidence_1.000_Length_827
+TGGGGTTGGCTTGAAACCAGCTTTGGGGGGTTCGATTCCTTCCTTTTTTGTCTAGATTTT
+ATGTATACGGGTTCTTCGAATGTGTGGTAGGGTGGGGGGCATCCATATAGTCACTCCAGG
+TTTATGGAGGGTTCTTCTACTATTAGGACTTTTCGCTTCGAAGCGAAGGCTTCTCAAATC
+ATGAAAATTATTAATATTACTGCTGTTAGAGAAATGAATGAGCCTACAGATGATAGGATG
+TTTCATGTGGTGTATGCATCGGGGTAGTCCGAGTAACGTCGGGGCATTCCGGATAGGCCG
+AGAAAGTGTTGTGGGAAGAAAGTTAGATTTACGCCGATGAATATGATAGTGAAATGGATT
+TTGGCGTAGGTTTGGTCTAGGGTGTAGCCTGAGAATAGGGGAAATCAGTGAATGAAGCCT
+CCTATGATGGCAAATACAGCTCCTATTGATAGGACATAGTGGAAGTGAGCTACAACGTAG
+TACGTGTCGTGTAGTACGATGTCTAGTGATGAGTTTGCTAATACAATGCCAGTCAGGCCA
+CCTACGGTGAAAAGAAAGATGAATCCTAGGGCTCAGAGCACTGCAGCAGATCATTTCATA
+TTGCTTCCGTGGAGTGTGGCGAGTCAGCTAAATACTTTGACGCCGGTGGGGATAGCGATG
+ATTATGGTAGCGGAGGTGAAATATGCTCGTGTGTCTACGTCTATTCCTACTGTAAATATA
+TGGTGTGCTCACACGATAAACCCTAGGAAGCCAATTGATATCATAGCTCAGACCATACCT
+ATGTATCCAAATGGTTCTTTTTTTCCGGAGTAGTAAGTTACAATATG
+>Locus_9_Transcript_1/1_Confidence_1.000_Length_131
+TCTAGTCATCCTCGTCGGTCTTCTGCTTCTTGGTATCGACATCGTCATCCTCATCATCTT
+CAGCTGCCCGCTTGCCCGTAGCTGACTCAGCTTCCTCATCTTCATCTCCATCCTCTTCCT
+CACCACGGCCG
+>Locus_10_Transcript_1/1_Confidence_1.000_Length_115
+TGGAATGGGAGACCTGTTGGCCTGTGGGCCTCACCTGCCCCTCTGTTCTCTCCCCTCACA
+TCCTCCTGCCCAGCTCCTCACATACCCACACATTCCAGGGCTGGGGTGAGCCTGA
+>Locus_11_Transcript_1/1_Confidence_1.000_Length_153
+CCCCCGGTGTCCCCGCGAGGGGCCCGGGGCGGGGTCCGCCGGCCCTGCGGGCCGCCGGTG
+AAATACCACTACTCTGATCGTTTTTTCACTGACCCGGTGAGGCGGGGGGGCGAGCCCCGA
+GGGGCTCTCGCTTCTGGCGCCAAGCGCCCGGCC
+>Locus_12_Transcript_1/1_Confidence_1.000_Length_555
+CCCGGTCGTGTAGCGGTGAAAGTGGTTTGGTTTAGACGTCCGGGAATTGCATCTGTTTTT
+AAGCCTAATGTGGGGACAGCTCATGAGTGCAAGACGTCTTGTGATGTAATTATTATACGA
+ATGGGGGCTTCAATCGGGAGTACTACTCGATTGTCAACGTCAAGGAGTCGCAGGTCGCCT
+GGTTCTAGGAATAATGGGGGAAGTATGTAGGAGTTGAAGATTAGTCCGCCGTAGTCGGTG
+TACTCGTAGGTTCAGTACCATTGGTGGCCAATTGATTTGATGGTAAGGGAGGGATCGTTG
+ACCTCGTCTGTTATGTAAAGGATGCGTAGGGATGGGAGGGCGATGAGGACTAGGATGATG
+GCGGGCAGGATAGTTCAGACGGTTTCCATTTCCTGAGCGTCTGAGATGTTAGTATTAGTT
+AGTTTTGTTGTGAGTGTTAGGAAAAGGGCATACAGGACTAGGAAGCAGATAAGGAAAATG
+ATTATGAGGGCGTGATCATGAAAGGTGATAAGCTCTTCTATGATAGGGGAAGTAGCGTCT
+TGTAGACCTACTTGC
+>Locus_13_Transcript_1/1_Confidence_1.000_Length_306
+GCCGGAGTAGTAAGTTACAATATGGGAGATTATTCCGAAGCCTGGTAGGATAAGAATATA
+AACTTCAGGGTGACCGAAAAATCAGAATAGGTGTTGGTATAGAATGGGGTCTCCTCCTCC
+GGCGGGGTCGAAGAAGGTGGTGTTGAGGTTGCGGTCTGTTAGTAGTATAGTGATGCCAGC
+AGCTAGGACTGGGAGAGATAGGAGAAGTAGGACTGCTGTGATTAGGACGGATCAGACGAA
+GAGGGGCGTTTGGTATTGGGTTATGGCAGGGGGTTTTATATTGATAATTGTTGTGATGAA
+ATTGAT
+>Locus_14_Transcript_1/1_Confidence_1.000_Length_171
+GGCCACCAGGCGTTTAACCGACGCTTTCTTGTTGTTGCGGAATAATTCCATCCAAAACCG
+GCAGCTGTTAGCCGAGCAAGTTCAAAATGAGCCTGTTTGGAACAACCTCAGGTTTTGGAA
+CCAGTGGGACCAGCATGTTTGGCAGTGCAACTACAGACAATCACAATCCCA
+>Locus_16_Transcript_1/1_Confidence_1.000_Length_109
+AGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAAAG
+GTAGCATAATCACTTGTTCCTTAAATAGGGCCCTGTATGAATGGCTCCA
+>Locus_17_Transcript_1/1_Confidence_1.000_Length_138
+GACCTGCTAGGGTGAGAAGGATTATTCGAGTGCTATAGGCGCTTGTCAGGGAGGTAGCGA
+TGAGAGTAATAGATAGGGCTCAGGCGTTTGTGTATGATATGTTTGCGGTTTCGATGATGT
+GGTCTTTGGAGTAGAAAC
+>Locus_19_Transcript_1/1_Confidence_1.000_Length_232
+CTAACCGGCTTTTTGCCCAAATGAGCCATTATCGAAGAATTCACAAAAAACAATAGCCTC
+ATCATCCCCACCATCATAGCCACCATCACCCTCCTTAACCTCTACTTCTACCTACGCCTA
+ATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAACGTAAAAATAAAATGACAG
+TTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATCGCCCTTACCA
+>Locus_20_Transcript_1/1_Confidence_1.000_Length_350
+GGCGGGTCCGGGCCCATGAGGCGACGAAGGAGGCGGGACGGCTTTTACCCAGCCCCGGAC
+TTCCGAGACAGGGAAGCTGAGGACATGGCAGGAGTGTTTGACATAGACCTGGACCAGCCA
+GAGGACGCGGGCTCTGAGGATGAGCTGGAGGAGGGGGCCAAGTATAAGGAGCGAGGGACG
+GTCTTGGCTGAGGACCAGCTAGCCCAGATGTCAAAGCAGTTGGACATGTTCAAGACCAAC
+CTGGAGGAATTTGCCAGCAAACACAAGCAGGAGATCCGGAAGAATCCTGAGTTCCGTGTG
+CAGTTCCAGGACATGTGTGCAACCATTGGCGTGGATCCGCTGGCCTCTGG
+>Locus_21_Transcript_1/2_Confidence_0.667_Length_119
+TGTAGATCCAAGTGTGGAAGGCTGACCTTGCATCCATGGCAACCATAAAGTAGGGTCCAT
+GACTCTTCTCTCCCTTTCTCTCTCTTTTCTCCACACTCGGAGAACATGGGCAGTTTTTT
+>Locus_21_Transcript_2/2_Confidence_0.667_Length_222
+TGTAGATCCAAGTGTGGAAGGCTGACCTTGCATCCATGGCAACCATAAAGTAGGGTCCAT
+GACTCTTCTCTCCCTTTCTCTCTCTTTTCTCCACACTTTGAAAGGAGGATGTGTGGACCC
+TTTCTCCTATATGCTTATGTCTCTGTTGTCGTAGATTGGCGTCCTTTGTGAGCTATTCAG
+TGACATTTCAGAACCATTTTGCTCTGCAGAAAACCCGCAGTT
+>Locus_22_Transcript_1/1_Confidence_1.000_Length_302
+GGTTGTTGATGAGATATTTGGAGGAGGCCTAGTAGTGGGGTGAGGCTTGGATTAGCGTTT
+AGAAGGGCTATTTGTTGTGGGTCTCATGAGTTGGAGTGTAGGATAAATCATGCTAAGGCG
+AGGATGAAACCGATATCGCCGATACGGTTGTATAGGATTGCTTGAATGGCTGCTGTGTTG
+GCATCTGCTCGGGCGTATCATCAACTGATGAGCAAGAAGGATATAATTCCTACGCCCTCT
+CAGCCGATGAACAGTTGGAATAGGTTGTTAGCGGTAACTAAGATTAGTATGGTAATTAGG
+AA
+>Locus_24_Transcript_1/1_Confidence_1.000_Length_308
+GACCGGTCCCCGCCTTTTTGTAAAACTTAAAGCGGGCGCAGCATTAACGCTTCCCGCCCC
+GGTGACCTCTCAGGGGTCTCCCCGCCAAAGGTGCTCCGCCGCTAAGGAACATGGCGAAGG
+TGGAGCAGGTCCTGAGCCTCGAGCCGCAGCACGAGCTCAAATTCCGAGCAAGTGCGGAGG
+CAAGACACATCAAAGCAGAGATGGGAAGTGAAAGAGCTCTCGTACTGGACAGATTAGCAA
+GCAATGTGGCAAAACGAAAAAGCTCAATGCCTCAGAAATTCATTGGTGAGAAGCGCCACT
+GCTTTGAT
+>Locus_25_Transcript_1/1_Confidence_1.000_Length_101
+CATGATCCTGCAATAAGAAAGTTCCCCGGCAAGGTTGGTGGGCTAAAAGACAGACAACCA
+ATGCTATCATCAGGAGATGATGTTACTTCAATATCCTTCAT
+>Locus_26_Transcript_1/1_Confidence_1.000_Length_201
+CGCCGCTCCCGACCCTCCCGCGCCCCCGCCCTGCCGCGCTGCTCCCCGCCCAGCCGCGGG
+TCTGTGGTCCAAGCCGCCCCGAAGCAGCCCCCAGATGAAAACTCGCTGGATTTTTCCTCC
+TGTATGTTACGGCCTGGGATTAAAAATGCTCAGGAGCTTGCCTGTGGAGTGTGCCTCTTG
+AATGTGGACTCGAGGAGCCGG
+>Locus_27_Transcript_1/1_Confidence_1.000_Length_421
+TAAGATTTGCCGAGTTCCTTTTACTTTTTTTAACCTTTCCTTATGAGCATGCCTGTGTTG
+GGTTGACAGTGAGGGTAATAATGACTTGTTGGTTGATTGTAGATATTGGGCTGTTAATTG
+TCAGTTCAGTGTTTTAATCTGACGCAGGCTTATGCGGAGGAGAATGTTTTCATGTTACTT
+ATACTAACATTAGTTCTTCTATAGGGTGATAGATTGGTCCAATTGGGTGTGAGGAGTTCA
+GTTATATGTTTGGGATTTTTTAGGTAGTGGGTGTTGAGCTTGAACGCTTTCTTAATTGGT
+GGCTGCTTTTAGGCCTACTATGGGTGTTAAATTTTTTACTCTCTCTACAAGGTTTTTTCC
+TAGTGTCCAAAGAGCTGTTCCTCTTTGGACTAACAGTTAAATTTACAAGTGGATTTAGAG
+G
+>Locus_28_Transcript_1/1_Confidence_1.000_Length_343
+AGAGAGGGAGGTAAGAGTCAGAAGCTTATGTTGTTTATGCGGGGAAACGCCATATCGGGG
+GCACCGATTATTAGGGGAACTAGTCAGTTGCCAAAGCCTCCGATTATGATGGGTATTACT
+ATGAAGAAGATTATTACAAATGCATGGGCTGTGACGATAACGTTGTAGATGTGGTCGTTA
+CCTAGAAGGTTGCCTGGCTGGCCCAGCTCGGCTCGAATAAGGAGGCTTAGAGCTGTGCCT
+AGGACTCCAGCTCATGCGCCGAATAATAGGTATAGTGTTCCAATGTCTTTGTGGTTTGTA
+GAGAATAGTCAACGGTCGGCGAACATCAGTGGGGGTGAGGTAA
+>Locus_29_Transcript_1/1_Confidence_1.000_Length_119
+GAGATGATATACAGGTTTTTGGCTCCTGTGTTGTCAGCACAATTGATTACAGCTCCTACC
+GGAAGACCCAAGGAAATCCGGAATTTCGCACCAGAGGACCCACCACGTCCTCGCTTCGA
+>Locus_32_Transcript_1/1_Confidence_1.000_Length_180
+CGGCCGCAGCCATGAGTATGCTCAGGCTTCAGAAGAGGCTCGCCTCTAGTGTCCTCCGCT
+GTGGCAAGAAGAAGGTCTGGTTAGACCCCAATGAGACCAATGAAATCGCCAATGCCAACT
+CCCGTCAGCAGATCCGGAAGCTCATCAAAGATGGGCTGATCATCCGCAAGCCTGTGACGG
+>Locus_33_Transcript_1/1_Confidence_1.000_Length_127
+ACTCCTGCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCC
+TCCCTTAGCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTT
+ACACCTA
+>Locus_35_Transcript_1/1_Confidence_1.000_Length_307
+CCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCT
+CATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAA
+ACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCT
+AACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGG
+ATTCTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACCACAAGGCA
+CACCTAC
+>Locus_36_Transcript_1/1_Confidence_1.000_Length_246
+CTTGTTTTATTTTAATGGCTGATCTATGTAATCACAGAGGCCAGTATGTACAGACAAAGT
+GGGAGGTTTTATTTCTTGGTCTCTTCCTCCTTGGATAAAGTCTTGATGATCTCCTCCTTC
+TTGGCCTGGAGGCGCTCTTCACGGCGCTTGCGTGCTTCCTTGGTCTTAGACCTGCGGGCC
+TCAGCCTGGTCAGCCAGGAGCTTCTTGCGGGCCTTGTCTGCCTTCAGCTTGTGGATGTGT
+TCCATG
+>Locus_37_Transcript_1/1_Confidence_1.000_Length_172
+TCTCACTGTGGGTTCTGAGGAAACTCTCAGGGGAAGACAGCTCTTCATACCCTCACATAA
+CCCCACCCACACACAGGCCCAGAGACACCTACAGACACACCCCCGCCCCATCTCTCACAC
+TCACACTCACACACTTGCGTGTCAGACACCTGCAGACATACATGCTCCTGCC
+>Locus_38_Transcript_1/1_Confidence_1.000_Length_212
+ACGGGATGGATCCAGGATGTAGTCTGTGTTACATGATTGATGAAGTACTTGATTCCATCT
+GCTGTGTAAGCTTCCTCCCACCCATAAGGTAAACCCTCGGTTTCCCCCTGAGCTTTCATC
+CTGAAGGCGAGGAGAAGCTAGATCCGCCACAAAAGGATAAGCCCTTCCCCACCACTAACG
+GAGGAAACAAGTTGGCTCGGGATCCCGGGACG
+>Locus_40_Transcript_1/1_Confidence_1.000_Length_132
+CCCTGGGCAATGACGTCTTCAATGTTTTTTCCATTCAGCTCACTGATAACCTTGTTGAGC
+CGGTCGTCGTCCGCCTCGATACCCACGCTGTCCAAGATCTTCTTGATGTCCTTGGCGCTG
+GGGGAGGAGTTG
+>Locus_41_Transcript_1/1_Confidence_1.000_Length_194
+TAGGATCCTCTACGCACAACGCCTGCTCGCCTCCTCCGTGTGGTTGCCAAGCCAAGCCGC
+CTGCTACCTTCATCACCAAATTGCACTCGCTCCTTCCTGGAATCCTTTTTCCTAGCTTCA
+CCACCAAATCGTTAGCGCTCCTTCCTTCTTCCTAGCTTCCTTCACCAAATCGCACTGGCT
+CCTGGACTCTTTTC
+>Locus_43_Transcript_1/1_Confidence_1.000_Length_109
+TGGAATTAAGGGTGTTAGTCATGTTAGCTTGTTTCAGGTGCGAGATAGTAGTAGGGTCGT
+GGTGCTGGAGTTTAAGTTGAGTAGTAGGAATGCGGTAGTAGTTAGGATA
+>Locus_44_Transcript_1/1_Confidence_1.000_Length_339
+GGGTGTGAGCCCGGCCCGTGGCGGCCACGTCTCCCGGGAGATGCTGTGACGGACCCGCAC
+GGGAGGAGCTCGCGCCTGGCCTGGCGACCCGGTGGACTCGGCCCGCGGCGGCGCGCTCAC
+CCGCCCCGTTCAGATAAAGGCTGGTGGTGGGAGAATGCTATCGCTGCCCTGTTTCGGAGA
+CACATTCCCGTCAGCTGGCTGATCCGCGCTACCCTGAGTGAGTCGGAAAACTTCGAAGCA
+GCTGTTGGCAAGTTGGCCAAGACTCCCCTTATTGCTGATGTTTATTACATTGTTGGTGGC
+ACGTCCCCCCGGGAGGGGGTGGTCATCACGAGGAACAGA
+>Locus_45_Transcript_1/1_Confidence_1.000_Length_121
+AGACCCTATGGAGCTTTAATTTATTAATGCAAGCAGTACCTAACAAACCCACAGGTCCTA
+AACTACCAAACCTGCATTAAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTC
+C
+>Locus_46_Transcript_1/1_Confidence_1.000_Length_122
+GGTCTTCTCGTCTTGCTGTGTCATGCCCGCCTCTTCACGGGCAGGTCAATTTCACTGGTT
+AAAAGTAAGAGACAGCTGAACCCTCGTGGAGCCATTCATACAGGTCCCTATTTAAGGAAC
+AA
+>Locus_47_Transcript_1/1_Confidence_1.000_Length_156
+GGGCACTCTCTGCCTGGGTCCGTTCTTCTTCCCTCTGGGCCTGGATGGCCTCCATTTCTG
+TCTGCTGCTCCTTTAGCCTCATTTCCAGCTCCATTTTTTCCCTTTCTAAGCTCTCCAGAG
+CCTTTGCCAGCTCCTGCTGGTGCCAGGAGCGCTCCT
+>Locus_48_Transcript_1/1_Confidence_1.000_Length_185
+GTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCT
+ATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGAC
+CCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAA
+AATAG
+>Locus_50_Transcript_1/1_Confidence_1.000_Length_125
+TCCGAACCCCCTCATGATTCTCGATTTTGCTGATAATCTTGATGTTCTTTCCCTTCTCTC
+CCAGGACCTTCCTAACTTCATGGACATCAGATGCCTTGCGGATGAATGACGCAAACACCA
+TATCA
+>Locus_51_Transcript_1/1_Confidence_1.000_Length_187
+GTCCACGCTTTCTGCCTTCTGCTCCACAGTGTCCTCAGGGAAGTGCGCGAATGTCACGGG
+ACTGTTCTCTGTGGTTCCATAAGCAACCTTAGCTGCTGTACAAGCTCCGGACAGCTCACA
+GGATTCTCCCCATGGTGAGCCACTTTTACATCACAAAGCTGTCCTGCAGGATCTAACTGC
+ACTTCCA
diff -r 000000000000 -r 854531fa1645 tool-data/ctat_genome_ref_libs.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/ctat_genome_ref_libs.loc.sample	Thu Apr 12 10:52:54 2018 -0400
@@ -0,0 +1,15 @@
+# This file lists the locations of CTAT Genome Reference Libraries
+# Usually there will only be one library, but it is concievable 
+# that there could be multiple libraries.
+# This file format is as follows
+# (white space characters are TAB characters):
+#
+#<value>    <name>  <path>
+# value is a unique id
+# name is the display name
+# path is the directory where the genome lib files are stored
+#
+#ctat_genome_ref_libs.loc could look like:
+#
+#GRCh38_v27_CTAT_lib_Feb092018	CTAT_GenomeRefLib_GRCh38_v27_CTAT_lib_Feb092018	/ctat/genome/reference/lib/path
+#
diff -r 000000000000 -r 854531fa1645 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Apr 12 10:52:54 2018 -0400
@@ -0,0 +1,10 @@
+<tables>
+    <table name="ctat_genome_ref_libs" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, name, path</columns>
+        <file path="tool-data/ctat_genome_ref_libs.loc" />
+    </table>
+    <table name="ctat_centrifuge_indexes" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, name, path</columns>
+        <file path="tool-data/ctat_centrifuge_indexes.loc" />
+    </table>
+</tables>