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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 11:41:55 -0500
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643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 #This is a sample file distributed with Galaxy that enables tools
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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2 #to use a directory of 2bit genome files for use with Lastz. You will
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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3 #need to supply these files and then create a lastz_seqs.loc file
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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4 #similar to this one (store it in this directory) that points to
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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5 #the directories in which those files are stored. The lastz_seqs.loc
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 #file has this format (white space characters are TAB characters):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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7 #
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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8 #<unique_build_id> <display_name> <file_path>
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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9 #
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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10 #So, for example, if your lastz_seqs.loc began like this:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 #
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 #hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13 #hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 #mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15 #
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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16 #then your /depot/data2/galaxy/twobit/ directory
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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17 #would need to contain the following 2bit files:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 #
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.2bit
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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22 #
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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23 #Your lastz_seqs.loc file should include an entry per line for
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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24 #each file you have stored that you want to be available. Note that
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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25 #your files should all have the extension '2bit'.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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26 #
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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27 #Note that for backwards compatibility with workflows, the unique ID of
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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28 #an entry must be the path that was in the original loc file, because that
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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29 #is the value stored in the workflow for that parameter.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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30 #