Mercurial > repos > sanbi-uwc > freebayes

annotate tool-data/all_fasta.loc.sample @ 7:9d88d9f45a7f draft default tip

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit 935873f98b4ec40c6db2e91e27ac483afc8c4af4
author sanbi-uwc
date Tue, 08 May 2018 08:53:21 -0400
parents 2cd1943090d2
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2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
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1 #This is a sample file distributed with Galaxy that enables tools
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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2 #to use a directory of Samtools indexed sequences data files. You will need
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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3 #to create these data files and then create a fasta_indexes.loc file
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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4 #similar to this one (store it in this directory) that points to
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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5 #the directories in which those files are stored. The fasta_indexes.loc
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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6 #file has this format (white space characters are TAB characters):
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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7 #
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
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8 # <unique_build_id> <dbkey> <display_name> <file_base_path>
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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9 #
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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10 #So, for example, if you had hg19 Canonical indexed stored in
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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11 #
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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12 # /depot/data2/galaxy/hg19/sam/,
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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13 #
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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14 #then the fasta_indexes.loc entry would look like this:
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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15 #
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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17 #
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
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18 #and your /depot/data2/galaxy/hg19/sam/ directory
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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19 #would contain hg19canon.fa and hg19canon.fa.fai files.
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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20 #
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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21 #Your fasta_indexes.loc file should include an entry per line for
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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22 #each index set you have stored. The file in the path does actually
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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23 #exist, but it should never be directly used. Instead, the name serves
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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24 #as a prefix for the index file. For example:
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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25 #
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
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26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
sanbi-uwc
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28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
2cd1943090d2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty
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29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa