Mercurial > repos > iuc > samtools_cram_to_bam

annotate tool-data/fasta_indexes.loc.sample @ 0:0637018367e0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:18:56 -0400
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0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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1 #This is a sample file distributed with Galaxy that enables tools
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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2 #to use a directory of Samtools indexed sequences data files. You will need
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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3 #to create these data files and then create a fasta_indexes.loc file
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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4 #similar to this one (store it in this directory) that points to
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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5 #the directories in which those files are stored. The fasta_indexes.loc
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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6 #file has this format (white space characters are TAB characters):
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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7 #
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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8 # <unique_build_id> <dbkey> <display_name> <file_base_path>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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9 #
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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10 #So, for example, if you had hg19 Canonical indexed stored in
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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11 #
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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12 # /depot/data2/galaxy/hg19/sam/,
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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13 #
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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14 #then the fasta_indexes.loc entry would look like this:
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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15 #
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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17 #
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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18 #and your /depot/data2/galaxy/hg19/sam/ directory
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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19 #would contain hg19canon.fa and hg19canon.fa.fai files.
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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20 #
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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21 #Your fasta_indexes.loc file should include an entry per line for
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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22 #each index set you have stored. The file in the path does actually
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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23 #exist, but it should never be directly used. Instead, the name serves
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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24 #as a prefix for the index file. For example:
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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25 #
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa