Mercurial > repos > iuc > checkm2_build_database

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit 3e15f64954fb060e11abfe1a6857c21f4032ad9c
author iuc
date Mon, 06 Oct 2025 16:41:35 +0000
parents 757826aa89c3
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34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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1 #This is a sample file distributed with Galaxy that enables tools
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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2 #to use a the checkm2 dabase.
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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3 #You will need to create these data files using the following command
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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5 #checkm2 database --download --path /custom/path/
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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7 #and then create a checkm2_db_versioned.loc file similar to this one (store it in this
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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8 #directory) that points to the directories in which those files are stored.
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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10 #The checkm2_db_versioned.loc file has this format (longer white space
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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11 #characters are TAB characters):
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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12 #
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757826aa89c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit 043f6bb449b27287b413a937b21d918569cfdad7
iuc
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13 #<unique_build_id> <dbkey> <display_name> <version> <file_base_path>
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34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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15 #The <version> column indicates the checkm2 version that generated the database
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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17 #
2
757826aa89c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit 043f6bb449b27287b413a937b21d918569cfdad7
iuc
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18 #diamond_db_1.0.2 1.0.2 Diamond database 1.0.2 /mnt/galaxyIndices/Checkm2_database/uniref100.KO.1.dmnd