annotate all_fasta.loc.sample @ 5:8b62f89924a7 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 64bbe6ec9a3f3cd6241fa4cf0e0548e0e67629a0"
author iuc
date Sat, 18 Jan 2020 12:59:37 -0500
parents 3fd7458bc861
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
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1 #This file lists the locations and dbkeys of all the fasta files
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
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2 #under the "genome" directory (a directory that contains a directory
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
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3 #for each build). The script extract_fasta.py will generate the file
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
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4 #all_fasta.loc. This file has the format (white space characters are
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
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5 #TAB characters):
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
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6 #
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
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8 #
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
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9 #So, all_fasta.loc could look something like this:
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
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10 #
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
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14 #
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
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15 #Your all_fasta.loc file should contain an entry for each individual
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
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16 #fasta file. So there will be multiple fasta files for each build,
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
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17 #such as with hg19 above.
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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18 #