# HG changeset patch
# User rhpvorderman
# Date 1506324926 14400
# Node ID 5f8d9309058ba6b1909d8a81a0c28512a3cb9c81
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
diff -r 000000000000 -r 5f8d9309058b data_manager/data_manager_select_index_by_path.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_select_index_by_path.xml Mon Sep 25 03:35:26 2017 -0400
@@ -0,0 +1,52 @@
+
+ path inputer
+
+ path_name_value_key_manager.py
+ --value "${value}"
+ --dbkey "${dbkey}"
+ --name "${name}"
+ --path "${path}"
+ --data_table_name "${data_table}"
+ --json_output_file "${json_output_file}"
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+Adds a server path to the selected data table.
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+The tool will check the path exists but NOT check that it holds the expected data type.
+
+If name is not provided the filename from path less the extension is used.
+
+If value is not provided, the name will be used (or its default)
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+If dbkey is not provided, the value will be used (or its default)
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diff -r 000000000000 -r 5f8d9309058b data_manager/indexes.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/indexes.yml Mon Sep 25 03:35:26 2017 -0400
@@ -0,0 +1,50 @@
+all_fasta:
+ name: fasta file
+ extensions:
+ - .fa
+ no_prefix: True
+bowtie2_indexes:
+ name: bowtie2 index
+ extensions:
+ - .bt2
+bowtie_indexes:
+ name: bowtie index
+ extensions:
+ - .ebwt
+bowtie_indexes_color:
+ name: bowtie color index
+ extensions:
+ - .ebwt
+bwa_mem_indexes:
+ name: bwa mem index
+ extensions:
+ - .amb
+ - .ann
+ - .bwt
+ - .pac
+ - .sa
+bwameth_indexes:
+ name: bwa_meth_index
+fasta_indexes:
+ name: fasta index
+ extensions:
+ - .fai
+gatk_picard_index:
+ name: picard index for GATK
+gene_transfer:
+ name: Gene Transfer File
+ extensions:
+ - .gtf
+hisat2_indexes:
+ name: hisat2 index
+ extensions:
+ - .ht2
+kallisto_indexes:
+ name: kallisto index
+ no_prefix: True
+picard_indexes:
+ name: picard index
+tophat2_indexes:
+ name: tophat2 index
+ extensions:
+ - .bt2
diff -r 000000000000 -r 5f8d9309058b data_manager/path_name_value_key_manager.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/path_name_value_key_manager.py Mon Sep 25 03:35:26 2017 -0400
@@ -0,0 +1,104 @@
+#!/usr/bin/env python
+
+import json
+import argparse
+import os
+import yaml
+
+def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
+ data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+ data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
+ data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
+ return data_manager_dict
+
+
+def check_param(name, value, default=None, check_tab=True):
+ if value in [ None, '', '?' ]:
+ if default:
+ print "Using {0} for {1} as no value provided".format( default, name )
+ value = default
+ else:
+ raise Exception( '{0} is not a valid {1}. You must specify a valid {1}.'.format( value, name ) )
+ if check_tab and "\t" in value:
+ raise Exception( '{0} is not a valid {1}. It may not contain a tab because these are used as seperators by galaxy .'.format( value, name ) )
+ return value
+
+def prefix_exists(directory, prefix):
+ '''checks if files exist with prefix in a directory. Returns Boolean'''
+ matched_files = []
+ directory_files = os.listdir(directory)
+ for directory_file in directory_files:
+ if directory_file.startswith(prefix):
+ matched_files.append(directory_file)
+ # Empty list should return False
+ return bool(matched_files)
+
+def prefix_plus_extension_exists(directory, prefix, extension):
+ '''checks if files exist with prefix in a directory. Returns Boolean'''
+ matched_files = []
+ directory_files = os.listdir(directory)
+ for directory_file in directory_files:
+ if directory_file.startswith(prefix) and directory_file.endswith(extension):
+ matched_files.append(directory_file)
+ # Empty list should return False
+ return bool(matched_files)
+
+def main():
+
+ #value = "test_value"
+ #name = "test_name"
+ #print '{0} other {1} more{0}'.format(value, name )
+ #print '{0} is not a valid {1}. It may not contain a tab.'.format( value, name )
+
+ #Parse Command Line
+ parser = argparse.ArgumentParser()
+ parser.add_argument( '--value', action='store', type=str, default=None, help='value' )
+ parser.add_argument( '--dbkey', action='store', type=str, default=None, help='dbkey' )
+ parser.add_argument( '--name', action='store', type=str, default=None, help='name' )
+ parser.add_argument( '--path', action='store', type=str, default=None, help='path' )
+ parser.add_argument( '--data_table_name', action='store', type=str, default=None, help='path' )
+ parser.add_argument( '--json_output_file', action='store', type=str, default=None, help='path' )
+ options = parser.parse_args()
+
+ path = check_param("path", options.path)
+ basename = os.path.basename(path)
+ filename = os.path.splitext(basename)[0]
+ name = check_param("name", options.name, default=filename)
+ value = check_param("value", options.value, default=name)
+ dbkey = check_param("dbkey", options.dbkey, default=value)
+ data_table_name = check_param("data_table_name", options.data_table_name)
+ json_output_file = check_param("json_output_file", options.json_output_file, check_tab=False)
+
+ # Check if file or prefix exists
+ indexes = yaml.load(file(os.path.join(os.path.dirname(__file__), 'indexes.yml')))
+ index_dict = indexes.get(data_table_name,{})
+ index_name = index_dict.get('name','index')
+ index_extensions = index_dict.get('extensions', [''])
+ no_prefix = index_dict.get('no_prefix', False)
+ if not no_prefix:
+ dirname = os.path.dirname(path)
+ prefix = basename
+ for extension in index_extensions:
+ if not prefix_plus_extension_exists(dirname,prefix,extension):
+ raise Exception( 'Unable to find files with prefix "{0}" and extension "{1}" in {2}. Is this a valid {3}?'.format( prefix, extension, dirname, index_name ) )
+ else:
+ if not os.path.exists(path):
+ raise Exception( 'Unable to find path {0}.'.format( path ) )
+
+ if os.path.exists(json_output_file):
+ params = json.loads( open( json_output_file ).read() )
+ print "params", params
+ else:
+ params = {}
+
+ data_manager_dict = {}
+ data_table_entry = dict( value=value, dbkey=dbkey, name=name, path=path )
+ _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
+
+ #save info to json file
+ with open( json_output_file, 'wb' ) as output_file:
+ output_file.write( json.dumps( data_manager_dict ) )
+ output_file.write( "\n" )
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r 5f8d9309058b data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Mon Sep 25 03:35:26 2017 -0400
@@ -0,0 +1,110 @@
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diff -r 000000000000 -r 5f8d9309058b test.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.json Mon Sep 25 03:35:26 2017 -0400
@@ -0,0 +1,1 @@
+{"data_tables": {"all_fasta": [{"path": "test-data/EboVir3.fa", "dbkey": "EboVir3", "name": "EboVir3", "value": "EboVir3"}]}}
diff -r 000000000000 -r 5f8d9309058b tool-data/all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample Mon Sep 25 03:35:26 2017 -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 5f8d9309058b tool-data/bowtie2_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bowtie2_indices.loc.sample Mon Sep 25 03:35:26 2017 -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 5f8d9309058b tool-data/bowtie_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bowtie_indices.loc.sample Mon Sep 25 03:35:26 2017 -0400
@@ -0,0 +1,37 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Bowtie indexed sequences data files. You will
+#need to create these data files and then create a bowtie_indices.loc
+#file similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bowtie_indices.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#
+#
+#So, for example, if you had hg18 indexed stored in
+#/depot/data2/galaxy/bowtie/hg18/,
+#then the bowtie_indices.loc entry would look like this:
+#
+#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18
+#
+#and your /depot/data2/galaxy/bowtie/hg18/ directory
+#would contain hg18.*.ebwt files:
+#
+#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt
+#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt
+#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt
+#...etc...
+#
+#Your bowtie_indices.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files. For example:
+#
+#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon
+#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full
+#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
diff -r 000000000000 -r 5f8d9309058b tool-data/bowtie_indices_color.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bowtie_indices_color.loc.sample Mon Sep 25 03:35:26 2017 -0400
@@ -0,0 +1,37 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Bowtie indexed sequences data files. You will
+#need to create these data files and then create a bowtie_indices.loc
+#file similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bowtie_indices.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#
+#
+#So, for example, if you had hg18 indexed stored in
+#/depot/data2/galaxy/bowtie/hg18/,
+#then the bowtie_indices.loc entry would look like this:
+#
+#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18
+#
+#and your /depot/data2/galaxy/bowtie/hg18/ directory
+#would contain hg18.*.ebwt files:
+#
+#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt
+#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt
+#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt
+#...etc...
+#
+#Your bowtie_indices.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files. For example:
+#
+#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon
+#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full
+#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
diff -r 000000000000 -r 5f8d9309058b tool-data/bwa_mem_index.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bwa_mem_index.loc.sample Mon Sep 25 03:35:26 2017 -0400
@@ -0,0 +1,38 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of BWA indexed sequences data files. You will need
+#to create these data files and then create a bwa_index.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bwa_index.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#
+#
+#So, for example, if you had phiX indexed stored in
+#/depot/data2/galaxy/phiX/base/,
+#then the bwa_index.loc entry would look like this:
+#
+#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa
+#
+#and your /depot/data2/galaxy/phiX/base/ directory
+#would contain phiX.fa.* files:
+#
+#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb
+#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann
+#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt
+#...etc...
+#
+#Your bwa_index.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files. For example:
+#
+#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa
+#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa
+#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa
+#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
diff -r 000000000000 -r 5f8d9309058b tool-data/bwameth_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bwameth_indexes.loc.sample Mon Sep 25 03:35:26 2017 -0400
@@ -0,0 +1,15 @@
+# This is a sample file distributed with Galaxy that is used to define a
+# list of bwa-meth indices, using three columns tab separated:
+#
+#
+#
+# An index can be created with the following command:
+#
+# bwameth.py index /some/path/genome.fa
+#
+# "/some/path/genome.fa" would then be the last column in the line
+# If this were for the mm10 mouse genome, the resulting entry would look like:
+#
+#mm9 mm9 Mouse (mm9) /some/path/genome.fa
+#
+#
diff -r 000000000000 -r 5f8d9309058b tool-data/fasta_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample Mon Sep 25 03:35:26 2017 -0400
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files. You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+#
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored. The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file. For example:
+#
+#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r 000000000000 -r 5f8d9309058b tool-data/gatk_sorted_picard_index.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gatk_sorted_picard_index.loc.sample Mon Sep 25 03:35:26 2017 -0400
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Picard dict and associated files. You will need
+#to create these data files and then create a picard_index.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The picard_index.loc
+#file has this format (longer white space is the TAB character):
+#
+#
+#
+#So, for example, if you had hg18 indexed and stored in
+#/depot/data2/galaxy/srma/hg18/,
+#then the srma_index.loc entry would look like this:
+#
+#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa
+#
+#and your /depot/data2/galaxy/srma/hg18/ directory
+#would contain the following three files:
+#hg18.fa
+#hg18.dict
+#hg18.fa.fai
+#
+#The dictionary file for each reference (ex. hg18.dict) must be
+#created via Picard (http://picard.sourceforge.net). Note that
+#the dict file does not have the .fa extension although the
+#path list in the loc file does include it.
+#
diff -r 000000000000 -r 5f8d9309058b tool-data/gene_transfer.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gene_transfer.loc.sample Mon Sep 25 03:35:26 2017 -0400
@@ -0,0 +1,14 @@
+#This file lists the locations and dbkeys of all the gene transfer files
+
+#This file has the format (white space characters are TAB characters):
+#
+#
+#
+#So, gene_transfer.loc could look something like this:
+#
+#vm5 vm5 vM5 annotation /path/to/vM5.annotation.gtf
+#
+#Your gene_transfer.loc file should contain an entry for each individual
+#gtf file.
+#
+
diff -r 000000000000 -r 5f8d9309058b tool-data/hisat2_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/hisat2_indexes.loc.sample Mon Sep 25 03:35:26 2017 -0400
@@ -0,0 +1,39 @@
+# hisat2_indexes.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 HISAT2.
+# 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 hisat2_indexes.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 sacCer3 indexes stored in:
+#
+# /depot/data2/galaxy/sacCer3/hisat2_indexes/
+#
+# containing sacCer3 genome and sacCer3.*.ht2 files, such as:
+#
+# -rw-rw-r-- 1 dave dave 12M Sep 23 13:57 sacCer3.1.ht2
+# -rw-rw-r-- 1 dave dave 2.9M Sep 23 13:57 sacCer3.2.ht2
+# -rw-rw-r-- 1 dave dave 161 Sep 23 13:57 sacCer3.3.ht2
+# -rw-rw-r-- 1 dave dave 2.9M Sep 23 13:57 sacCer3.4.ht2
+# -rw-rw-r-- 1 dave dave 7.3M Sep 23 13:57 sacCer3.5.ht2
+# -rw-rw-r-- 1 dave dave 3.0M Sep 23 13:57 sacCer3.6.ht2
+# -rw-rw-r-- 1 dave dave 128K Sep 23 13:57 sacCer3.7.ht2
+# -rw-rw-r-- 1 dave dave 32K Sep 23 13:57 sacCer3.8.ht2
+#
+# then the hisat2_indexes.loc entry could look like this:
+#
+#sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/hisat2_indexes/sacCer3
+#
+#More examples:
+#
+#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/hisat2_indexes/mm10
+#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/hisat2_indexes/dm3
+#
+#
diff -r 000000000000 -r 5f8d9309058b tool-data/kallisto_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/kallisto_indexes.loc.sample Mon Sep 25 03:35:26 2017 -0400
@@ -0,0 +1,33 @@
+# kallisto_indexes.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 kallisto.
+# 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 kallisto_indexes.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 sacCer3 indexes stored in:
+#
+# /depot/data2/galaxy/sacCer3/kallisto_indexes/
+#
+# containing sacCer3 genome and sacCer3.*.ht2 files, such as:
+#
+# -rw-rw-r-- 1 dave dave 12M Sep 23 13:57 sacCer3.fa
+# -rw-rw-r-- 1 dave dave 2.9M Sep 23 13:57 sacCer3.kallisto
+#
+# then the kallisto_indexes.loc entry could look like this:
+#
+#sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/kallisto_indexes/sacCer3.kallisto
+#
+#More examples:
+#
+#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/kallisto_indexes/mm10
+#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/kallisto_indexes/dm3
+#
+#
diff -r 000000000000 -r 5f8d9309058b tool-data/picard_index.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/picard_index.loc.sample Mon Sep 25 03:35:26 2017 -0400
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Picard dict and associated files. You will need
+#to create these data files and then create a picard_index.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The picard_index.loc
+#file has this format (longer white space is the TAB character):
+#
+#
+#
+#So, for example, if you had hg18 indexed and stored in
+#/depot/data2/galaxy/srma/hg18/,
+#then the srma_index.loc entry would look like this:
+#
+#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa
+#
+#and your /depot/data2/galaxy/srma/hg18/ directory
+#would contain the following three files:
+#hg18.fa
+#hg18.dict
+#hg18.fa.fai
+#
+#The dictionary file for each reference (ex. hg18.dict) must be
+#created via Picard (http://picard.sourceforge.net). Note that
+#the dict file does not have the .fa extension although the
+#path list in the loc file does include it.
+#
diff -r 000000000000 -r 5f8d9309058b tool-data/tophat2_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tophat2_indices.loc.sample Mon Sep 25 03:35:26 2017 -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 5f8d9309058b tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Mon Sep 25 03:35:26 2017 -0400
@@ -0,0 +1,55 @@
+
+
+