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add tool_data_table_conf (bowti2) to the repenrich wrapper (#682)
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* add tool_data_table_conf (bowti2)

* add EOL
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drosofff authored Apr 20, 2024
1 parent 4dd520d commit 4ac0720
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2 changes: 1 addition & 1 deletion tools/repenrich2/macros.xml
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<macros>
<token name="@TOOL_VERSION@">2.31.1</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@VERSION_SUFFIX@">2</token>
<token name="@PROFILE@">23.0</token>

<xml name="repenrich_requirements">
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37 changes: 37 additions & 0 deletions tools/repenrich2/tool-data/bowtie2_indices.loc.sample
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# 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
#
#
8 changes: 8 additions & 0 deletions tools/repenrich2/tool_data_table_conf.xml.sample
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<!-- 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>
<!-- Locations of indexes in the Bowtie2 mapper format -->
<table name="bowtie2_indexes" comment_char="#">
<columns>value, dbkey, name, path</columns>
<file path="tool-data/bowtie2_indices.loc" />
</table>
</tables>

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