Mercurial > repos > iuc > jbrowse
annotate tool-data/all_fasta.loc.sample @ 20:558d652cd681 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75a0a1c7b26cac156f76e8266a0e2e3d81be7f02
author | iuc |
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date | Thu, 30 Aug 2018 11:43:59 -0400 |
parents | f422ba2e9aa5 |
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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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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
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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
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6 # |
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
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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
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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
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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
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14 # |
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
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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
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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
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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 # |