Mercurial > repos > timpalpant > java_genomics_toolkit

annotate sam_fa_indices.loc.sample @ 25:b43c420a6135 draft default tip

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Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
author timpalpant
date Sat, 09 Feb 2019 14:02:24 -0500
parents 35031c567ece
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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16
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
parents:
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1 #This is a sample file distributed with Galaxy that enables tools
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
parents:
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2 #to use a directory of Samtools indexed sequences data files. You will need
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
parents:
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3 #to create these data files and then create a sam_fa_indices.loc file
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
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4 #similar to this one (store it in this directory) that points to
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
parents:
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5 #the directories in which those files are stored. The sam_fa_indices.loc
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
parents:
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6 #file has this format (white space characters are TAB characters):
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
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7 #
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
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8 #index <seq> <location>
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
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9 #
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
parents:
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10 #So, for example, if you had hg18 indexed stored in
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
parents:
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11 #/depot/data2/galaxy/sam/,
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
parents:
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12 #then the sam_fa_indices.loc entry would look like this:
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
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13 #
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
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14 #index hg18 /depot/data2/galaxy/sam/hg18.fa
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
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15 #
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
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16 #and your /depot/data2/galaxy/sam/ directory
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
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17 #would contain hg18.fa and hg18.fa.fai files:
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
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18 #
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
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19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
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20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
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21 #
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
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22 #Your sam_fa_indices.loc file should include an entry per line for
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
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23 #each index set you have stored. The file in the path does actually
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
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24 #exist, but it should never be directly used. Instead, the name serves
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
timpalpant
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25 #as a prefix for the index file. For example:
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
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26 #
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
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27 #index hg18 /depot/data2/galaxy/sam/hg18.fa
35031c567ece Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
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28 #index hg19 /depot/data2/galaxy/sam/hg19.fa