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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
author iuc
date Thu, 24 Sep 2020 15:11:57 +0000
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c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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1 #This is a sample file distributed with Galaxy that enables tools
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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2 #to use a directory of Samtools indexed sequences data files. You will need
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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3 #to create these data files and then create a fasta_indexes.loc file
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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4 #similar to this one (store it in this directory) that points to
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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5 #the directories in which those files are stored. The fasta_indexes.loc
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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6 #file has this format (white space characters are TAB characters):
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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7 #
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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8 # <unique_build_id> <dbkey> <display_name> <file_base_path>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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9 #
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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10 #So, for example, if you had hg19 Canonical indexed stored in
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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11 #
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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12 # /depot/data2/galaxy/hg19/sam/,
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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13 #
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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14 #then the fasta_indexes.loc entry would look like this:
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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15 #
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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17 #
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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18 #and your /depot/data2/galaxy/hg19/sam/ directory
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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19 #would contain hg19canon.fa and hg19canon.fa.fai files.
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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20 #
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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21 #Your fasta_indexes.loc file should include an entry per line for
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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22 #each index set you have stored. The file in the path does actually
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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23 #exist, but it should never be directly used. Instead, the name serves
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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24 #as a prefix for the index file. For example:
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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25 #
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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26 test_buildid hg17 test_displayname ${__HERE__}/genome.fasta