annotate all_fasta.loc.sample @ 3:2a57d2ef04c6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
author iuc
date Fri, 20 Mar 2020 05:15:40 -0400
parents 872249f5495a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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1 #This file lists the locations and dbkeys of all the fasta files
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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2 #under the "genome" directory (a directory that contains a directory
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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3 #for each build). The script extract_fasta.py will generate the file
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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4 #all_fasta.loc. This file has the format (white space characters are
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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5 #TAB characters):
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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6 #
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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8 #
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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9 #So, all_fasta.loc could look something like this:
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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10 #
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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14 #
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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15 #Your all_fasta.loc file should contain an entry for each individual
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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16 #fasta file. So there will be multiple fasta files for each build,
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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17 #such as with hg19 above.
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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18 #