Mercurial > repos > rhpvorderman > data_manager_select_index_by_path
changeset 0:5f8d9309058b draft
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
line wrap: on
line diff
--- /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 @@ +<tool id="data_manager_select_index_by_path" name="Select index by path manager" tool_type="manage_data" version="0.0.2"> + <description>path inputer</description> + <command interpreter="python"> + 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}" + </command> + <inputs> + <param name="value" type="text" value="" label="value field for the entry. Defaults to name if left blank." /> + <param name="dbkey" type="text" value="" label="dbkey field for the entry. Defaults to value if left blank." /> + <param name="name" type="text" value="" label="name field for the entry. Defaults to the file name from path if left blank." /> + <param name="path" type="text" value="" label="path field for the entry" /> + <param name="data_table" type="select" value="" label="data table for the index"> + <option value='all_fasta'>all_fasta</option> + <option value='bowtie2_indexes'>bowtie2_indexes</option> + <option value='bowtie_indexes'>bowtie_indexes</option> + <option value='bowtie_indexes_color'>bowtie_indexes_color</option> + <option value='bwa_mem_indexes'>bwa_mem_indexes</option> + <option value='bwameth_indexes'>bwameth_indexes</option> + <option value='fasta_indexes'>fasta_indexes</option> + <option value='gatk_picard_indexes'>gatk_picard_indexes</option> + <option value='gene_transfer'>gene_transfer</option> + <option value='hisat2_indexes'>hisat2_indexes</option> + <option value='kallisto_indexes'>kallisto_indexes</option> + <option value='picard_indexes'>picard_indexes</option> + <option value='tophat2_indexes'>tophat2_indexes</option> + </param> + </inputs> + <outputs> + <data name="json_output_file" format="data_manager_json"/> + </outputs> + + <help> +Adds a server path to the selected data table. + +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) + +If dbkey is not provided, the value will be used (or its default) + + </help> + <citations> + </citations> + +</tool>
--- /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
--- /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()
--- /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 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/data_manager_select_index_by_path.xml" id="data_manager_select_index_by_path" version="0.0.2"> + <data_table name="all_fasta"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" /> + </output> + </data_table> + <data_table name="bowtie2_indexes"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" /> + </output> + </data_table> + <data_table name="bowtie_indexes"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" /> + </output> + </data_table> + <data_table name="bowtie_indexes_color"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" /> + </output> + </data_table> + <data_table name="bwa_mem_indexes"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" /> + </output> + </data_table> + <data_table name="bwameth_indexes"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" /> + </output> + </data_table> + <data_table name="fasta_indexes"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" /> + </output> + </data_table> + <data_table name="gatk_picard_indexes"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" /> + </output> + </data_table> + <data_table name="gene_transfer"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" /> + </output> + </data_table> + <data_table name="hisat2_indexes"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" /> + </output> + </data_table> + <data_table name="kallisto_indexes"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" /> + </output> + </data_table> + <data_table name="picard_indexes"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" /> + </output> + </data_table> + <data_table name="tophat2_indexes"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" /> + </output> + </data_table> + </data_manager> + +</data_managers>
--- /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"}]}}
--- /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): +# +#<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. +#
--- /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. +# +# <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 +# +#
--- /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): +# +#<unique_build_id> <dbkey> <display_name> <file_base_path> +# +#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. +#
--- /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): +# +#<unique_build_id> <dbkey> <display_name> <file_base_path> +# +#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. +#
--- /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): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#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. +#
--- /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: +# +# <unique_build_id> <dbkey> <display_name> <genome_fasta_file_path> +# +# 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 +# +#
--- /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): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#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
--- /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): +# +#<unique_build_id> <dbkey> <display_name> <fasta_file_path> +# +#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. +#
--- /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): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#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. +# +
--- /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. +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +# 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 +# +#
--- /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. +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +# 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 +# +#
--- /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): +# +#<unique_build_id> <dbkey> <display_name> <fasta_file_path> +# +#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. +#
--- /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. +# +# <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 +# +#
--- /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 @@ +<!-- 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> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> + <table name="bowtie2_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bowtie2_indices.loc" /> + </table> + <table name="bowtie_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bowtie_indices.loc" /> + </table> + <table name="bowtie_indexes_color" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bowtie_indices_color.loc" /> + </table> + <table name="bwa_mem_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bwa_mem_index.loc" /> + </table> + <table name="bwameth_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bwameth_indexes.loc" /> + </table> + <table name="fasta_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> + <table name="gatk_picard_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/gatk_sorted_picard_index.loc" /> + </table> + <table name="gene_transfer" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/gene_transfer.loc" /> + </table> + <table name="hisat2_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/hisat2_indexes.loc" /> + </table> + <table name="kallisto_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/kallisto_indexes.loc" /> + </table> + <table name="picard_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/picard_index.loc" /> + </table> + <table name="tophat2_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/tophat2_indices.loc" /> + </table> + </tables>