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annotate all_fasta.loc.sample @ 1:cd5f453e7364 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
author iuc
date Sat, 13 Aug 2016 04:40:03 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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cd5f453e7364 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
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1 #This file lists the locations and dbkeys of all the fasta files
cd5f453e7364 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
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2 #under the "genome" directory (a directory that contains a directory
cd5f453e7364 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
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3 #for each build). The script extract_fasta.py will generate the file
cd5f453e7364 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
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4 #all_fasta.loc. This file has the format (white space characters are
cd5f453e7364 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
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5 #TAB characters):
cd5f453e7364 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
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6 #
cd5f453e7364 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
cd5f453e7364 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
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8 #
cd5f453e7364 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
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9 #So, all_fasta.loc could look something like this:
cd5f453e7364 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
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10 #
cd5f453e7364 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
cd5f453e7364 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
cd5f453e7364 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
cd5f453e7364 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
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14 #
cd5f453e7364 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
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15 #Your all_fasta.loc file should contain an entry for each individual
cd5f453e7364 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
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16 #fasta file. So there will be multiple fasta files for each build,
cd5f453e7364 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
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17 #such as with hg19 above.
cd5f453e7364 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
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18 #