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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit a54e50916ebdb0858b049cdc549a43df801e1a71
author iuc
date Tue, 21 May 2024 07:36:22 +0000
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6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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1 # kallisto_indexes.loc.sample
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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2 # This is a *.loc.sample file distributed with Galaxy that enables tools
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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3 # to use a directory of indexed data files. This one is for kallisto.
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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4 # See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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5 # First create these data files and save them in your own data directory structure.
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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6 # Then, create a kallisto_indexes.loc file to use those indexes with tools.
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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7 # Copy this file, save it with the same name (minus the .sample),
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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8 # follow the format examples, and store the result in this directory.
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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9 # The file should include an one line entry for each index set.
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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10 # The path points to the "basename" for the set, not a specific file.
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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11 # It has four text columns seperated by TABS.
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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12 #
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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13 # <unique_build_id> <dbkey> <display_name> <file_base_path>
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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14 #
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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15 # So, for example, if you had sacCer3 indexes stored in:
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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16 #
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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17 # /depot/data2/galaxy/sacCer3/kallisto_indexes/
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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18 #
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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19 # containing sacCer3 genome and sacCer3.*.ht2 files, such as:
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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20 #
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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21 # -rw-rw-r-- 1 dave dave 12M Sep 23 13:57 sacCer3.fa
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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22 # -rw-rw-r-- 1 dave dave 2.9M Sep 23 13:57 sacCer3.kallisto
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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23 #
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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24 # then the kallisto_indexes.loc entry could look like this:
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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25 #
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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26 #sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/kallisto_indexes/sacCer3.kallisto
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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27 #
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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28 #More examples:
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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29 #
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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30 #mm10 mm10 Mouse (mm10) /depot/data2/galaxy/kallisto_indexes/mm10
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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31 #dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/kallisto_indexes/dm3
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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32 #
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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33 #