Mercurial > repos > iuc > dram_set_database_locations

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
author iuc
date Thu, 01 Sep 2022 17:14:59 +0000
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06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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1 <tool id="dram_set_database_locations" name="DRAM: set database locations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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2 <description>after installation by the data manager</description>
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3 <macros>
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4 <import>macros.xml</import>
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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5 </macros>
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6 <expand macro="requirements"/>
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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7 <command detect_errors="exit_code"><![CDATA[
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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8 python '$__tool_directory__/dram_set_database_locations.py'
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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9 $skip_uniref
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10 --db_version '$db_version'
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11 --galaxy_data_manager_data_path '$galaxy_data_manager_data_path'
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12 --output '$output'
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13 ]]></command>
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14 <inputs>
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15 <param argument="--skip_uniref" type="boolean" truevalue="--skip_uniref" falsevalue="" checked="false" label="Did you skip downloading and processing uniref when you installed the DRAM databases?"/>
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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16 <param name="db_version" type="text" value="1.3.5" label="DRAM database version">
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17 <expand macro="sanitizer"/>
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18 </param>
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19 <param name="galaxy_data_manager_data_path" type="text" value="" label="Absolute Galaxy data manager data path" help="This is the absolute path for the Galaxy tool-data config setting">
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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20 <expand macro="sanitizer"/>
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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21 </param>
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22 </inputs>
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23 <outputs>
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24 <data name="output" format="txt"/>
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25 </outputs>
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26 <tests>
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27 <test expect_failure="true">
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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28 <param name="skip_uniref" value="true"/>
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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29 <param name="galaxy_data_manager_data_path" value="/gx/tool-data"/>
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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30 <assert_stderr>
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31 <has_text text="error: unrecognized arguments: db: None"/>
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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32 </assert_stderr>
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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33 </test>
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34 </tests>
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35 <help>
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36 Use of this tool should be restricted to a Galaxy administrator. This tool updates the DRAM configuration file
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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37 with the location of the databases after installation by the data manager. This is necessary because DRAM creates
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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38 a configuration file during installation, but the file is written before the Galaxy job finishes, so the database
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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39 locations are relative to the job working directory instead of the configured GALAXY_DATA_MANAGER_DATA_PATH.
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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40
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41 It may be more ideal to perform this task as a second step in the data manager tool, but DRAM will not allow
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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42 the configuration file to be updated to point to locations unless the databases exist in those locations. But
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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43 the data manager tool moves the databases to these locations as its last step, making it impossible to update
06c5b883632d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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44 the DRAM configuration file as a second step of that tool.
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45
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46 See https://github.com/WrightonLabCSU/DRAM/wiki/5.-Managing%2C-updating-or-moving-a-DRAM-installation-and-databases for details.
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47 </help>
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48 <citations>
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49 <citation type="doi">10.1093/nar/gkaa621</citation>
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50 </citations>
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51 </tool>
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52