Mercurial > repos > blankenberg > naive_variant_caller

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"planemo upload for repository https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/master/tools/naive_variant_caller commit 6f2b4ed336036cd98c043536e45905bcd3c93044"
author blankenberg
date Thu, 05 Dec 2019 16:55:20 +0000
parents 0095f76a5d05
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0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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1 #This is a sample file distributed with Galaxy that enables tools
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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2 #to use a directory of Samtools indexed sequences data files. You will need
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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3 #to create these data files and then create a sam_fa_indices.loc file
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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4 #similar to this one (store it in this directory) that points to
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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5 #the directories in which those files are stored. The sam_fa_indices.loc
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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6 #file has this format (white space characters are TAB characters):
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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7 #
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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8 #index <seq> <location>
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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9 #
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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10 #So, for example, if you had hg18 indexed stored in
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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11 #/depot/data2/galaxy/sam/,
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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12 #then the sam_fa_indices.loc entry would look like this:
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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13 #
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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14 #index hg18 /depot/data2/galaxy/sam/hg18.fa
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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15 #
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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16 #and your /depot/data2/galaxy/sam/ directory
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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17 #would contain hg18.fa and hg18.fa.fai files:
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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18 #
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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21 #
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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22 #Your sam_fa_indices.loc file should include an entry per line for
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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23 #each index set you have stored. The file in the path does actually
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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24 #exist, but it should never be directly used. Instead, the name serves
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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25 #as a prefix for the index file. For example:
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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26 #
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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27 #index hg18 /depot/data2/galaxy/sam/hg18.fa
0095f76a5d05 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
blankenberg
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28 #index hg19 /depot/data2/galaxy/sam/hg19.fa