changeset 8:d2f4bfcf269a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"

--- a/data_manager/macros.xml	Thu Aug 15 11:28:53 2019 -0400
+++ b/data_manager/macros.xml	Thu Nov 28 20:32:41 2019 +0000
@@ -1,10 +1,11 @@
 <macros>
     <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager
     whenever you make changes to the following two version tokens!
-    The data manager uses a symlink to this macro file to keep the versions in
-    sync. -->
+    The data manager uses a symlink to this macro file to keep the STAR and
+    the index versions in sync, but you should manually adjust the +galaxy
+    version number. -->
     <!-- STAR version to be used -->
-    <token name="@VERSION@">2.7.2a</token>
+    <token name="@VERSION@">2.7.2b</token>
     <!-- STAR index version compatible with this version of STAR
     This is the STAR version that introduced the index structure expected
     by the current version.
@@ -18,10 +19,11 @@
         <requirements>
             <requirement type="package" version="@VERSION@">star</requirement>
             <requirement type="package" version="1.9">samtools</requirement>
+            <yield />
         </requirements>
     </xml>
 
-    <xml name="index_selection" token_with_gene_model="1">
+    <xml name="index_selection" token_with_gene_model="0">
         <param argument="--genomeDir" name="genomeDir" type="select"
         label="Select reference genome"
         help="If your genome of interest is not listed, contact the Galaxy team">
@@ -88,7 +90,7 @@
         &&
     #end if
     ]]></token>
-    <token name="@REFGENOMEHANDLING" ><![CDATA[
+    <token name="@REFGENOMEHANDLING@" ><![CDATA[
     --runThreadN \${GALAXY_SLOTS:-4}
     --genomeLoad NoSharedMemory
     --genomeDir
@@ -97,7 +99,7 @@
     #else:
         '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
         ## Handle difference between indices with/without annotations
-        #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
+        #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf':
             #if $refGenomeSource.GTFconditional.sjdbGTFfile:
                 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
                 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
@@ -114,6 +116,7 @@
             <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
             <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
             <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
+            <yield />
         </stdio>
     </xml>
     <xml name="refgenomehandling" >
@@ -127,16 +130,16 @@
                     <param name="GTFselect" type="select"
                            label="Reference genome with or without an annotation"
                            help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions.">
-                        <option value="without-gtf">use genome reference with builtin gene-model</option>
-                        <option value="with-gtf">use genome reference without builtin gene-model</option>
+                        <option value="without-gtf" selected='true'>use genome reference without builtin gene-model</option>
+                        <option value="with-gtf">use genome reference with builtin gene-model</option>
                     </param>
                     <when value="with-gtf">
+                        <expand macro="index_selection" with_gene_model="1" />
+                    </when>
+                    <when value="without-gtf">
                         <expand macro="index_selection" with_gene_model="0" />
                         <expand macro="@SJDBOPTIONS@" />
                     </when>
-                    <when value="without-gtf">
-                        <expand macro="index_selection" with_gene_model="1" />
-                    </when>
                 </conditional>
             </when>
             <when value="history">

--- a/data_manager/rna_star_index_builder.py	Thu Aug 15 11:28:53 2019 -0400
+++ b/data_manager/rna_star_index_builder.py	Thu Nov 28 20:32:41 2019 +0000
@@ -6,26 +6,42 @@
 
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument( '--config-file' )
-    parser.add_argument( '--value' )
-    parser.add_argument( '--dbkey' )
-    parser.add_argument( '--name' )
-    parser.add_argument( '--subdir' )
-    parser.add_argument( '--data-table' )
-    parser.add_argument( '--with-gene-model', action='store_true' )
-    parser.add_argument( '--index-version' )
+    parser.add_argument('--config-file')
+    parser.add_argument('--value')
+    parser.add_argument('--dbkey')
+    parser.add_argument('--name')
+    parser.add_argument('--subdir')
+    parser.add_argument('--data-table')
+    parser.add_argument('--with-gene-model', action='store_true')
+    parser.add_argument('--index-version')
 
     args = parser.parse_args()
 
-    if args.dbkey in [ None, '', '?' ]:
-        raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( args.dbkey ) )
+    if args.dbkey in [None, '', '?']:
+        raise Exception(
+            '"%s" is not a valid dbkey. You must specify a valid dbkey.'
+            % (args.dbkey)
+        )
 
     with_gene_model = "0"
     if args.with_gene_model:
         with_gene_model = "1"
 
-    data_manager_dict = {'data_tables': {args.data_table: [dict({"value": args.value, "dbkey": args.dbkey, "name": args.name, "path": args.subdir, "with_gene_model": with_gene_model, "version": args.index_version} )]}}
-    open( args.config_file, 'w' ).write( json.dumps( data_manager_dict ) )
+    data_manager_dict = {
+        'data_tables': {
+            args.data_table: [
+                {
+                    "value": args.value,
+                    "dbkey": args.dbkey,
+                    "name": args.name,
+                    "path": args.subdir,
+                    "with_gene_model": with_gene_model,
+                    "version": args.index_version
+                }
+            ]
+        }
+    }
+    open(args.config_file, 'w').write(json.dumps(data_manager_dict, sort_keys=True))
 
 
 if __name__ == "__main__":

--- a/data_manager/rna_star_index_builder.xml	Thu Aug 15 11:28:53 2019 -0400
+++ b/data_manager/rna_star_index_builder.xml	Thu Nov 28 20:32:41 2019 +0000
@@ -1,11 +1,13 @@
-<tool id="rna_star_index_builder_data_manager" name="rnastar index2" tool_type="manage_data" version="2.7.1a" profile="17.01">
+<tool id="rna_star_index_builder_data_manager" name="rnastar index2" tool_type="manage_data" version="@IDX_VERSION@+galaxy2" profile="19.05">
     <description>builder</description>
 
     <macros>
         <import>macros.xml</import>
     </macros>
 
-    <expand macro="requirements" />
+    <expand macro="requirements">
+        <requirement type="package" version="3.7">python</requirement>
+    </expand>
 
     <command><![CDATA[
 if [ -z "\$GALAXY_MEMORY_MB" ] ; then
@@ -14,17 +16,16 @@
     GALAXY_MEMORY_BYTES=\$((GALAXY_MEMORY_MB * 1000000)) ;
 fi ;
 
-#import json, os
-#set params = json.loads(open(str($out_file)).read())
-#set target_directory = $params['output_data'][0]['extra_files_path'].encode('ascii', 'replace')
-#set subdir = os.path.basename(target_directory)
+#import os
+#set $target_directory = str($out_file.extra_files_path)
+#set $subdir = os.path.basename($target_directory)
 
-mkdir -p '${target_directory}/${subdir}' &&
+mkdir '${target_directory}' &&
 
 STAR
 --runMode genomeGenerate
 --genomeFastaFiles '${all_fasta_source.fields.path}'
---genomeDir '${target_directory}/${subdir}'
+--genomeDir '${target_directory}'
 --limitGenomeGenerateRAM \${GALAXY_MEMORY_BYTES}
 #if $GTFconditional.GTFselect == "withGTF":
     --sjdbGTFfile '${GTFconditional.sjdbGTFfile}'
@@ -100,25 +101,26 @@
         <data name="out_file" format="data_manager_json"/>
     </outputs>
 
-    <!-- not available in planemo at the moment of writing
     <tests>
         <test>
-            <param name="all_fasta_source" value="phiX.fa"/>
+            <param name="all_fasta_source" value="phiX174"/>
             <param name="sequence_name" value="phiX"/>
             <param name="sequence_id" value="minimal-settings"/>
             <param name="modelformat" value="None"/>
 
-            <output name="out_file" file="test_star_01.data_manager_json"/>
+            <output name="out_file" file="test_star_01.data_manager_json" compare="re_match"/>
         </test>
     </tests>
-    -->
 
     <help><![CDATA[
 .. class:: infomark
 
 *What it does*
 
-This is a Galaxy datamanager for the rna STAR gap-aware RNA aligner.
+This is a Galaxy data manager tool for the gap-aware RNA aligner STAR.
+
+This version of the tool builds STAR indices of the format first introduced
+with STAR version @IDX_VERSION@.
 
 Please read the fine manual - that and the google group are the places to learn about the options above.
 

--- a/data_manager_conf.xml	Thu Aug 15 11:28:53 2019 -0400
+++ b/data_manager_conf.xml	Thu Nov 28 20:32:41 2019 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <data_managers>
-    <data_manager tool_file="data_manager/rna_star_index_builder.xml" id="rna_star_index_builder">
+    <data_manager tool_file="data_manager/rna_star_index_builder.xml" id="rna_star_index_builder" version="0.0.6">
         <data_table name="rnastar_index2_versioned">
             <output>
                 <column name="value" />
@@ -12,9 +12,9 @@
                             out_file.extra_files_path is used as base by default
                             if no source, eg for type=directory, then refers to base 
                         -->
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rnastar/${version}/${dbkey}/${value}</target>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rnastar/${version}/${dbkey}/${value}/${path}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/rnastar/${version}/${dbkey}/${value}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/rnastar/${version}/${dbkey}/${value}/${path}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
                 <column name="with_gene_model" />

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc	Thu Nov 28 20:32:41 2019 +0000
@@ -0,0 +1,19 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>		<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3		/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19		Human (Homo sapiens): hg19 Canonical		/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19		Human (Homo sapiens): hg19 Full			/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
+phiX174	phiX174	phiX174	${__HERE__}/phiX174.fasta

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX174.fasta	Thu Nov 28 20:32:41 2019 +0000
@@ -0,0 +1,79 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_star_01.data_manager_json	Thu Nov 28 20:32:41 2019 +0000
@@ -0,0 +1,1 @@
+{"data_tables": {"rnastar_index2_versioned": \[{"dbkey": "phiX174", "name": "phiX174", "path": ".*", "value": "phiX174", "version": "2.7.1a", "with_gene_model": "0"}\]}}
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Thu Nov 28 20:32:41 2019 +0000
@@ -0,0 +1,12 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/all_fasta.loc" />
+    </table>
+    <!-- Locations of STAR indexes -->
+    <table name="rnastar_index2_versioned" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path, with_gene_model, version</columns>
+        <file path="${__HERE__}/test-data/rnastar_index2_versioned.loc" />
+    </table>
+</tables>