Mercurial > repos > devteam > data_manager_twobit_builder
annotate tool-data/lastz_seqs.loc.sample @ 6:b640d79b49cb draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
| author | iuc |
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| date | Thu, 28 Nov 2019 20:33:03 +0000 |
| parents | 26e3ae5f74ed |
| children |
| rev | line source |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
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changeset
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1 #This is a sample file distributed with Galaxy that enables tools |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
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2 #to use a directory of 2bit genome files for use with Lastz. You will |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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3 #need to supply these files and then create a lastz_seqs.loc file |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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4 #similar to this one (store it in this directory) that points to |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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5 #the directories in which those files are stored. The lastz_seqs.loc |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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6 #file has this format (white space characters are TAB characters): |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
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changeset
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7 # |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
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8 #<unique_build_id> <display_name> <file_path> |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
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9 # |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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10 #So, for example, if your lastz_seqs.loc began like this: |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
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11 # |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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12 #hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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13 #hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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14 #mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
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15 # |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
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16 #then your /depot/data2/galaxy/twobit/ directory |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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17 #would need to contain the following 2bit files: |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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18 # |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.2bit |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
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22 # |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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23 #Your lastz_seqs.loc file should include an entry per line for |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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24 #each file you have stored that you want to be available. Note that |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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25 #your files should all have the extension '2bit'. |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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26 # |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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27 #Note that for backwards compatibility with workflows, the unique ID of |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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28 #an entry must be the path that was in the original loc file, because that |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
diff
changeset
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29 #is the value stored in the workflow for that parameter. |
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26e3ae5f74ed
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
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30 # |