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annotate all_fasta.loc.sample @ 28:d0743cb18ed8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3b3c0f1ea1756b0b250b5eb91661f33f11cc9c6d
author iuc
date Fri, 22 Feb 2019 03:20:59 -0500
parents 1e74f16adaa1
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7
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
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1 #This file lists the locations and dbkeys of all the fasta files
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
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2 #under the "genome" directory (a directory that contains a directory
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
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3 #for each build). The script extract_fasta.py will generate the file
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
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4 #all_fasta.loc. This file has the format (white space characters are
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
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5 #TAB characters):
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
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6 #
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
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8 #
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
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9 #So, all_fasta.loc could look something like this:
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
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10 #
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
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14 #
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
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15 #Your all_fasta.loc file should contain an entry for each individual
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
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16 #fasta file. So there will be multiple fasta files for each build,
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
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17 #such as with hg19 above.
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
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18 #