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annotate tool-data/all_fasta.loc.sample @ 0:10e2ea79ec55 draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
author yhoogstrate
date Thu, 05 Nov 2015 10:00:19 -0500
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10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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1 #This file lists the locations and dbkeys of all the fasta files
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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2 #under the "genome" directory (a directory that contains a directory
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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3 #for each build). The script extract_fasta.py will generate the file
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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4 #all_fasta.loc. This file has the format (white space characters are
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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5 #TAB characters):
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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6 #
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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8 #
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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9 #So, all_fasta.loc could look something like this:
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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10 #
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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14 #
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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15 #Your all_fasta.loc file should contain an entry for each individual
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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17 #such as with hg19 above.
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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18 #