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annotate tool-data/all_fasta.loc.sample @ 39:fd5dbf0f732e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da"
author iuc
date Tue, 28 Apr 2020 10:01:04 -0400
parents f422ba2e9aa5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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9
f422ba2e9aa5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
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1 #This file lists the locations and dbkeys of all the fasta files
f422ba2e9aa5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
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2 #under the "genome" directory (a directory that contains a directory
f422ba2e9aa5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
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diff changeset
3 #for each build). The script extract_fasta.py will generate the file
f422ba2e9aa5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
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4 #all_fasta.loc. This file has the format (white space characters are
f422ba2e9aa5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
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5 #TAB characters):
f422ba2e9aa5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
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6 #
f422ba2e9aa5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
f422ba2e9aa5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
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8 #
f422ba2e9aa5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
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9 #So, all_fasta.loc could look something like this:
f422ba2e9aa5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
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10 #
f422ba2e9aa5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
f422ba2e9aa5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
f422ba2e9aa5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
f422ba2e9aa5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
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14 #
f422ba2e9aa5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
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15 #Your all_fasta.loc file should contain an entry for each individual
f422ba2e9aa5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
f422ba2e9aa5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
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17 #such as with hg19 above.
f422ba2e9aa5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
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18 #