Mercurial > repos > devteam > data_manager_twobit_builder

annotate tool-data/alignseq.loc.sample @ 6:b640d79b49cb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
author iuc
date Thu, 28 Nov 2019 20:33:03 +0000
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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
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1 #This is a sample file distributed with Galaxy that enables tools
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2 #to use alignment data stored as axt files (lines starting with "align")
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3 #or nib files (lines starting with "seq"). You will need to index
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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4 #them and then create an alignseq.loc file similar to this one (store
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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5 #it in this directory) that points to the directories in which those
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6 #alignments are stored. The "align" data referred to by the alignseq.loc
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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7 #file has this format (white space characters are TAB characters):
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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8 #
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9 #align <build1> <build2> <dir>
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10 #
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11 #So, for example, if you had hg18/bosTau2 alignment files stored in
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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12 #/depot/data2/galaxy/hg18/align/bosTau2, then the alignseq.loc entry
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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13 #would look like this:
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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14 #
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15 #align hg18 bosTau2 /depot/data2/galaxy/hg18/align/bosTau2
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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16 #
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17 #and your /depot/data2/galaxy/hg18/align/bosTau2 directory would
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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18 #contain all of your alignment files (e.g.):
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19 #
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20 #-rw-rw-r-- 1 nate galaxy 151842783 2006-01-08 01:00 chr10.axt
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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21 #-rw-rw-r-- 1 nate galaxy 79575 2006-01-08 01:00 chr10_random.axt
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22 #-rw-rw-r-- 1 nate galaxy 155015634 2006-01-08 01:01 chr11.axt
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23 #...etc...
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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24 #
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25 #Your alignseq.loc file should include an entry per line for each alignment
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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26 #file you have stored. For example:
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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27 #
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28 #align anoGam1 dm1 /depot/data2/galaxy/anoGam1/align/dm1
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29 #align anoGam1 dm2 /depot/data2/galaxy/anoGam1/align/dm2
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30 #align canFam1 hg17 /depot/data2/galaxy/canFam1/align/hg17
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31 #...etc...
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32 #
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33 #The "seq" data referred to by the alignseq.loc file has this
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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34 #format (white space characters are TAB characters):
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35 #
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36 #seq <build1> <dir>
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37 #
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38 #So, for example, if you had anoGam1 sequence files stored in
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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39 #/depot/data2/galaxy/anoGam1/seq, then the alignseq.loc entry
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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40 #would look like this:
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41 #
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42 #seq anoGam1 /depot/data2/galaxy/anoGam1/seq
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43 #and your seq anoGam1 /depot/data2/galaxy/anoGam1/seq directory would
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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44 #contain all of your sequence files (e.g.):
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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45 #
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46 #-rw-rw-r-- 1 nate galaxy 24397551 2006-06-26 12:51 chr2L.nib
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47 #-rw-rw-r-- 1 nate galaxy 31362964 2006-06-26 12:51 chr2R.nib
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48 #-rw-rw-r-- 1 nate galaxy 20642013 2006-06-26 12:51 chr3L.nib
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49 #-rw-rw-r-- 1 nate galaxy 26636071 2006-06-26 12:51 chr3R.nib
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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50 #
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51 #Your alignseq.loc file should include an entry per line for each sequence
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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52 #file you have stored. For example:
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53 #
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54 #seq anoGam1 /depot/data2/galaxy/anoGam1/seq
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55 #seq bosTau2 /depot/data2/galaxy/bosTau2/seq
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56 #seq bosTau3 /depot/data2/galaxy/bosTau3/seq
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57 #...etc...