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Migrated tool version 0.9 from old tool shed archive to new tool shed repository
author pcingola
date Tue, 07 Jun 2011 17:08:59 -0400
parents
children 2cf01e805427
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481a95ca5339 Migrated tool version 0.9 from old tool shed archive to new tool shed repository
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2 # Interval data is stored here
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3 data_dir = /usr/local/snpEff/data/
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5 # Store cache files here
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6 cache_dir = /tmp
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8 # Comma separated list of genomes
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9 genomes : hg37, mm37
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11 # For each genome 'XX' a set of attributes are defined:
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12 # - XX.genome : The name of this genome
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13 # - XX.chromosomes : A comma separated list of chromosome names
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14 # - XX.fasta_dir : The directory where fasta files of this genome are located
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15 # - XX.chromo_fasta_files : A comma separated list of the fasta files (one per chromosome).
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16 # WARNING: They must be in the same order as the XX.chromosomes list
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17 #
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18 # Note: Attributes XX.fasta_dir and XX.chromo_fasta_files are only needed if you are building the data
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19 # structures yourself. If you are using a pre-built file, you can leave both of them unassigned.
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22 # Human genome, version hg37
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23 hg37.genome : Human
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24 hg37.chromosomes : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y
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25 hg37.fasta_dir : /data/genomes/hg37/
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26 hg37.chromo_fasta_files : chr1.fa, chr2.fa, chr3.fa, chr4.fa, chr5.fa, chr6.fa, chr7.fa, chr8.fa, chr9.fa, chr10.fa, chr11.fa, chr12.fa, chr13.fa, chr14.fa, chr15.fa, chr16.fa, chr17.fa, chr18.fa, chr19.fa, chr20.fa, chr21.fa, chr22.fa, chrX.fa, chrY.fa
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28 # Mouse genome, version mm37
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29 mm37.genome : Mouse
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30 mm37.chromosomes : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, X, Y
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31 mm37.fasta_dir : /data/genomes/mm37/
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32 mm37.chromo_fasta_files : chr1.fa, chr2.fa, chr3.fa, chr4.fa, chr5.fa, chr6.fa, chr7.fa, chr8.fa, chr9.fa, chr10.fa, chr11.fa, chr12.fa, chr13.fa, chr14.fa, chr15.fa, chr16.fa, chr17.fa, chr18.fa, chr19.fa, chrX.fa, chrY.fa