Mercurial > repos > earlhaminst > lotus2
annotate tool-data/all_fasta.loc.sample @ 15:6e9fd3e0dcbb draft
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
author | earlhaminst |
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date | Fri, 11 Feb 2022 19:48:19 +0000 |
parents | cf56a6553385 |
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2
cf56a6553385
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents:
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1 #This file lists the locations and dbkeys of all the fasta files |
cf56a6553385
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents:
diff
changeset
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2 #under the "genome" directory (a directory that contains a directory |
cf56a6553385
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents:
diff
changeset
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3 #for each build). The script extract_fasta.py will generate the file |
cf56a6553385
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents:
diff
changeset
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4 #all_fasta.loc. This file has the format (white space characters are |
cf56a6553385
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents:
diff
changeset
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5 #TAB characters): |
cf56a6553385
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents:
diff
changeset
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6 # |
cf56a6553385
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents:
diff
changeset
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7 #<unique_build_id> <dbkey> <display_name> <file_path> |
cf56a6553385
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents:
diff
changeset
|
8 # |
cf56a6553385
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents:
diff
changeset
|
9 #So, all_fasta.loc could look something like this: |
cf56a6553385
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents:
diff
changeset
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10 # |
cf56a6553385
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents:
diff
changeset
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa |
cf56a6553385
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents:
diff
changeset
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa |
cf56a6553385
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents:
diff
changeset
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa |
cf56a6553385
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents:
diff
changeset
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14 # |
cf56a6553385
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents:
diff
changeset
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15 #Your all_fasta.loc file should contain an entry for each individual |
cf56a6553385
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents:
diff
changeset
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16 #fasta file. So there will be multiple fasta files for each build, |
cf56a6553385
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents:
diff
changeset
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17 #such as with hg19 above. |
cf56a6553385
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 4f154640ea9b8d9472307287f0ee6483649c9466"
earlhaminst
parents:
diff
changeset
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18 # |