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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
author iuc
date Sun, 16 Apr 2023 08:30:13 +0000
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d3eb4d51b285 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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1 # hisat2_indexes.loc.sample
d3eb4d51b285 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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2 # This is a *.loc.sample file distributed with Galaxy that enables tools
d3eb4d51b285 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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3 # to use a directory of indexed data files. This one is for HISAT2.
d3eb4d51b285 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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4 # See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
d3eb4d51b285 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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5 # First create these data files and save them in your own data directory structure.
d3eb4d51b285 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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6 # Then, create a hisat2_indexes.loc file to use those indexes with tools.
d3eb4d51b285 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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7 # Copy this file, save it with the same name (minus the .sample),
d3eb4d51b285 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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8 # follow the format examples, and store the result in this directory.
d3eb4d51b285 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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9 # The file should include an one line entry for each index set.
d3eb4d51b285 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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10 # The path points to the "basename" for the set, not a specific file.
d3eb4d51b285 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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11 # It has four text columns seperated by TABS.
d3eb4d51b285 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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12 #
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13 # <unique_build_id> <dbkey> <display_name> <file_base_path>
d3eb4d51b285 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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14 #
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15 # So, for example, if you had sacCer3 indexes stored in:
d3eb4d51b285 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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16 #
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17 # /depot/data2/galaxy/sacCer3/hisat2_indexes/
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18 #
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19 # containing sacCer3 genome and sacCer3.*.ht2 files, such as:
d3eb4d51b285 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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20 #
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21 # -rw-rw-r-- 1 dave dave 12M Sep 23 13:57 sacCer3.1.ht2
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22 # -rw-rw-r-- 1 dave dave 2.9M Sep 23 13:57 sacCer3.2.ht2
d3eb4d51b285 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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23 # -rw-rw-r-- 1 dave dave 161 Sep 23 13:57 sacCer3.3.ht2
d3eb4d51b285 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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24 # -rw-rw-r-- 1 dave dave 2.9M Sep 23 13:57 sacCer3.4.ht2
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25 # -rw-rw-r-- 1 dave dave 7.3M Sep 23 13:57 sacCer3.5.ht2
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26 # -rw-rw-r-- 1 dave dave 3.0M Sep 23 13:57 sacCer3.6.ht2
d3eb4d51b285 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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27 # -rw-rw-r-- 1 dave dave 128K Sep 23 13:57 sacCer3.7.ht2
d3eb4d51b285 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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28 # -rw-rw-r-- 1 dave dave 32K Sep 23 13:57 sacCer3.8.ht2
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29 #
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30 # then the hisat2_indexes.loc entry could look like this:
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31 #
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32 #sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/hisat2_indexes/sacCer3
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33 #
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34 #More examples:
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35 #
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36 #mm10 mm10 Mouse (mm10) /depot/data2/galaxy/hisat2_indexes/mm10
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37 #dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/hisat2_indexes/dm3
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38 #
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39 #