Mercurial > repos > mvdbeek > fermikit_variants

annotate all_fasta.loc.sample @ 2:b66e81e4ffc7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 116ee70903ea6766c155b7109a6a6e170ef5bf5a-dirty
author mvdbeek
date Mon, 02 Jan 2017 05:39:20 -0500
parents e82224e52876
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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e82224e52876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
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1 #This file lists the locations and dbkeys of all the fasta files
e82224e52876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
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2 #under the "genome" directory (a directory that contains a directory
e82224e52876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
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3 #for each build). The script extract_fasta.py will generate the file
e82224e52876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
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4 #all_fasta.loc. This file has the format (white space characters are
e82224e52876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
5 #TAB characters):
e82224e52876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
6 #
e82224e52876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
7 #<unique_build_id> <dbkey> <display_name> <file_path>
e82224e52876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
8 #
e82224e52876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
9 #So, all_fasta.loc could look something like this:
e82224e52876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
10 #
e82224e52876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
e82224e52876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
e82224e52876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
e82224e52876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
14 #
e82224e52876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
e82224e52876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
e82224e52876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
17 #such as with hg19 above.
e82224e52876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
18 #