Mercurial > repos > mvdbeek > fermi2

annotate all_fasta.loc.sample @ 4:a206c60df528 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
author mvdbeek
date Fri, 30 Dec 2016 12:10:15 -0500
parents c6b11ead6f1f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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c6b11ead6f1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
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1 #This file lists the locations and dbkeys of all the fasta files
c6b11ead6f1f 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
c6b11ead6f1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
c6b11ead6f1f 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
c6b11ead6f1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
5 #TAB characters):
c6b11ead6f1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
6 #
c6b11ead6f1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
c6b11ead6f1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
8 #
c6b11ead6f1f 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:
c6b11ead6f1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
10 #
c6b11ead6f1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
c6b11ead6f1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
c6b11ead6f1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
c6b11ead6f1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
14 #
c6b11ead6f1f 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
c6b11ead6f1f 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,
c6b11ead6f1f 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.
c6b11ead6f1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
parents:
diff changeset
18 #