# HG changeset patch
# User wolma
# Date 1563196427 14400
# Node ID a7169e7254c1238940a53e40b0fffc8a2e265e76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit fd18bdf0c66a87e5ffda1dcba60d8ef9bc73d1bf-dirty
diff -r 000000000000 -r a7169e7254c1 data_manager/bowtie2_index_builder.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/bowtie2_index_builder.py Mon Jul 15 09:13:47 2019 -0400
@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+# Dan Blankenberg
+from __future__ import print_function
+
+import argparse
+import os
+import subprocess
+import sys
+
+import yaml
+
+try:
+ from shlex import quote as cmd_quote
+except ImportError:
+ from pipes import quote as cmd_quote
+
+
+def build_bowtie2_index(fasta_filename, target_directory, index_id):
+ # TODO: allow multiple FASTA input files
+ fasta_base_name = os.path.split( fasta_filename )[-1]
+ sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
+ os.symlink( fasta_filename, sym_linked_fasta_filename )
+ args = ['bowtie2-build', sym_linked_fasta_filename, index_id]
+ proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
+ return_code = proc.wait()
+ if return_code:
+ print("Error building index.", file=sys.stderr)
+ sys.exit(return_code)
+ return [' '.join(cmd_quote(arg) for arg in args)]
+
+
+def main():
+ parser = argparse.ArgumentParser()
+ parser.add_argument('metadata')
+ parser.add_argument( '-t', '--target-directory', default=None)
+ args = parser.parse_args()
+
+ params = yaml.safe_load(open(args.metadata))
+ params['cmds'] = []
+ if args.target_directory:
+ if not os.path.isdir(args.target_directory):
+ os.mkdir(args.target_directory)
+ else:
+ args.target_directory = os.getcwd()
+
+ dbkey = params['dbkey']
+ if dbkey in [ None, '', '?' ]:
+ raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
+
+ # build the index
+ params['cmds'] += build_bowtie2_index(params['source'], args.target_directory, params['id'])
+ with open(args.metadata, 'w') as fo:
+ yaml.dump(params, fo, allow_unicode=False, default_flow_style=False)
+
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r a7169e7254c1 data_manager/bowtie2_index_builder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/bowtie2_index_builder.xml Mon Jul 15 09:13:47 2019 -0400
@@ -0,0 +1,95 @@
+
+ builder
+
+ pyyaml
+ bowtie2
+
+
+
+ 2.3.4.3
+ 2.3.4.3
+
+## use the ref genome's ID as default for the index ID
+#if not str($sequence_id).strip():
+ #set $sequence_id = $all_fasta_source.fields.dbkey
+#end if
+## use the ref genome's name as default for the index name
+#if not str($sequence_name).strip():
+ #set $sequence_name = $all_fasta_source.fields.name
+#end if
+
+
+
+
+@SET_DEFAULTS@
+source: '${all_fasta_source.fields.path}'
+dbkey: '${all_fasta_source.fields.dbkey}'
+description: '${all_fasta_source.fields.name}'
+id: '$sequence_id'
+name: '$sequence_name'
+version: 2
+
+
+@SET_DEFAULTS@
+{
+ "data_tables": {
+ "bowtie2_indexes": [
+ {
+ "value": "$sequence_id",
+ "dbkey": "$all_fasta_source.fields.dbkey",
+ "name": "$sequence_name",
+ "path": "$sequence_id"
+ }
+ ]
+ #if $tophat2:
+ ,
+ "tophat2_indexes": [
+ {
+ "value": "$sequence_id",
+ "dbkey": "$all_fasta_source.fields.dbkey",
+ "name": "$sequence_name",
+ "path": "$sequence_id"
+ }
+ ]
+ #end if
+ }
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
+
+
diff -r 000000000000 -r a7169e7254c1 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Mon Jul 15 09:13:47 2019 -0400
@@ -0,0 +1,35 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r a7169e7254c1 test-data/all_fasta.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc Mon Jul 15 09:13:47 2019 -0400
@@ -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):
+#
+#
+#
+#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
diff -r 000000000000 -r a7169e7254c1 test-data/bowtie2_data_manager.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bowtie2_data_manager.json Mon Jul 15 09:13:47 2019 -0400
@@ -0,0 +1,1 @@
+{"data_tables": {"tophat2_indexes": [{"path": "phiX174", "dbkey": "phiX174", "name": "phiX174", "value": "phiX174"}], "bowtie2_indexes": [{"path": "phiX174", "dbkey": "phiX174", "name": "phiX174", "value": "phiX174"}]}}
\ No newline at end of file
diff -r 000000000000 -r a7169e7254c1 test-data/bowtie2_indices.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bowtie2_indices.loc Mon Jul 15 09:13:47 2019 -0400
@@ -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.
+#
+#
+#
+# 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
+#
+#
diff -r 000000000000 -r a7169e7254c1 test-data/phiX174.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX174.fasta Mon Jul 15 09:13:47 2019 -0400
@@ -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
+
diff -r 000000000000 -r a7169e7254c1 test-data/tophat2_indices.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tophat2_indices.loc Mon Jul 15 09:13:47 2019 -0400
@@ -0,0 +1,37 @@
+# tophat2_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.
+#
+#
+#
+# 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
+#
+#
diff -r 000000000000 -r a7169e7254c1 tool-data/all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample Mon Jul 15 09:13:47 2019 -0400
@@ -0,0 +1,18 @@
+#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):
+#
+#
+#
+#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.
+#
diff -r 000000000000 -r a7169e7254c1 tool-data/bowtie2_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bowtie2_indices.loc.sample Mon Jul 15 09:13:47 2019 -0400
@@ -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.
+#
+#
+#
+# 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
+#
+#
diff -r 000000000000 -r a7169e7254c1 tool-data/tophat2_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tophat2_indices.loc.sample Mon Jul 15 09:13:47 2019 -0400
@@ -0,0 +1,37 @@
+# tophat2_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.
+#
+#
+#
+# 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
+#
+#
diff -r 000000000000 -r a7169e7254c1 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Mon Jul 15 09:13:47 2019 -0400
@@ -0,0 +1,18 @@
+
+
+
+
+ value, dbkey, name, path
+
+
+
+
+ value, dbkey, name, path
+
+
+
+
+ value, dbkey, name, path
+
+
+
diff -r 000000000000 -r a7169e7254c1 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Mon Jul 15 09:13:47 2019 -0400
@@ -0,0 +1,17 @@
+
+
+
+ value, dbkey, name, path
+
+
+
+
+ value, dbkey, name, path
+
+
+
+
+ value, dbkey, name, path
+
+
+