Mercurial > repos > bgruening > deeptools_compute_gc_bias

annotate tool-data/deepTools_seqs.loc.sample @ 13:7cdfa7e071d7 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
author bgruening
date Mon, 15 Feb 2016 10:05:37 -0500
parents eac27e339763
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eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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1 #This is a sample file distributed with Galaxy that enables tools
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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2 #to use a directory of 2bit genome files for use with deepTools. You will
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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3 #need to supply these files and then create a deepTools_seqs.loc file
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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4 #similar to this one (store it in this directory) that points to
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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5 #the directories in which those files are stored. The deepTools_seqs.loc
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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6 #file has this format:
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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7 #
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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8 #<unique_build_id> <display_name> <file_path>
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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9 #
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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10 #So, for example, if your deepTools_seqs.loc began like this:
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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11 #
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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12 #hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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13 #hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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14 #mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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15 #
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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16 #then your /depot/data2/galaxy/twobit/ directory
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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17 #would need to contain the following 2bit files:
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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18 #
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.2bit
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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22 #
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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23 #Your deepTools_seqs.loc file should include an entry per line for
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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24 #each file you have stored that you want to be available. Note that
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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25 #your files should all have the extension '2bit'.
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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26 #
eac27e339763 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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27 #Please note that the <unique_build_id> is also used as "Species name abbreviation".