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annotate samtools_view/tool-data/fasta_indexes.loc.sample @ 2:e9df5e7da8b1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit f10a2b16814f61326750364c497ad143cac3d137-dirty
author matthias
date Mon, 25 Feb 2019 03:57:40 -0500
parents a115324acff0
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a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
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1 #This is a sample file distributed with Galaxy that enables tools
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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2 #to use a directory of Samtools indexed sequences data files. You will need
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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3 #to create these data files and then create a fasta_indexes.loc file
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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4 #similar to this one (store it in this directory) that points to
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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5 #the directories in which those files are stored. The fasta_indexes.loc
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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6 #file has this format (white space characters are TAB characters):
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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7 #
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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8 # <unique_build_id> <dbkey> <display_name> <file_base_path>
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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9 #
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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10 #So, for example, if you had hg19 Canonical indexed stored in
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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11 #
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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12 # /depot/data2/galaxy/hg19/sam/,
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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13 #
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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14 #then the fasta_indexes.loc entry would look like this:
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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15 #
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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17 #
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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18 #and your /depot/data2/galaxy/hg19/sam/ directory
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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19 #would contain hg19canon.fa and hg19canon.fa.fai files.
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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20 #
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
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21 #Your fasta_indexes.loc file should include an entry per line for
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
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22 #each index set you have stored. The file in the path does actually
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
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23 #exist, but it should never be directly used. Instead, the name serves
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
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24 #as a prefix for the index file. For example:
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
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25 #
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
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26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
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27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
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28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
a115324acff0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
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29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa