Mercurial > repos > morinlab > sequenza

annotate tool-data/fasta_indexes.loc.sample @ 3:235c8e5dfece draft default tip

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author morinlab
date Sun, 29 Jan 2017 11:42:51 -0500
parents 73338a1805e7
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73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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1 #This is a sample file distributed with Galaxy that enables tools
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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2 #to use a directory of Samtools indexed sequences data files. You will need
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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3 #to create these data files and then create a fasta_indexes.loc file
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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4 #similar to this one (store it in this directory) that points to
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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5 #the directories in which those files are stored. The fasta_indexes.loc
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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6 #file has this format (white space characters are TAB characters):
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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7 #
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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8 # <unique_build_id> <dbkey> <display_name> <file_base_path>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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9 #
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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10 #So, for example, if you had hg19 Canonical indexed stored in
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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11 #
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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12 # /depot/data2/galaxy/hg19/sam/,
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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13 #
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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14 #then the fasta_indexes.loc entry would look like this:
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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15 #
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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17 #
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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18 #and your /depot/data2/galaxy/hg19/sam/ directory
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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19 #would contain hg19canon.fa and hg19canon.fa.fai files.
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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20 #
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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21 #Your fasta_indexes.loc file should include an entry per line for
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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22 #each index set you have stored. The file in the path does actually
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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23 #exist, but it should never be directly used. Instead, the name serves
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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24 #as a prefix for the index file. For example:
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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25 #
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa