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1 #This is a sample file that enables the segemehl mapper to find genome indices
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2 #and database files. You will need to create these data files and then create
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3 #a segemehl_indices.loc file similar to this one (store it in this directory)
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4 #that points to the directories in which those files are stored.
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5 #The segemehl_indices.loc file has this format (longer white space characters are TAB characters):
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6 #
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7 #<unique_build_id> <dbkey> <display_name> <file_base_path>
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8 #
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9 #So, for example, if you had hg18 indexed stored in
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10 #/data/0/galaxy/segemehl/hg18/,
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11 #then the segemehl_indices.loc entry would look like this:
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12 #
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13 #hg18 hg18 hg18 /data/0/galaxy/segemehl/hg18/chromosomes.fa /data/0/galaxy/segemehl/hg18/chromosomes.idx
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14 #
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15 #and your /data/0/galaxy/segemehl/hg18/ directory
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16 #would contain hg18.*.ebwt files:
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17 #
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18 #-rw-r--r-- 1 bag bag 539833 2013-10-13 10:12 chromosomes.idx
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19 #-rw-r--r-- 1 bag bag 342562 2013-10-13 10:12 chromosomes.fa
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20 #...etc...
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21 #
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22 #Your segemehl_indices.loc file should include an entry per line for each
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23 #index set you have stored. The "file" in the path does not actually
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24 #exist, but it is the prefix for the actual index files. For example:
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25 #
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26 #hg18canon hg18 hg18 Canonical /data/0/galaxy/segemehl/hg18/chromosomes_can.fa /data/0/galaxy/segemehl/hg18/chromosomes_can.idx
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27 #hg18full hg18 hg18 Full /data/0/galaxy/segemehl/hg18/chromosomes_full.fa /data/0/galaxy/segemehl/hg18/chromosomes_full.idx
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28 #...etc...
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29 #
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