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1 # This is a sample file distributed with Galaxy that enables tools
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2 # to use gene/exon annotations in the GFF/GTF format. You will need
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3 # to add all the gene set annotations in this configuration file.
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4 # Because of this file, galaxy tools are able to access gene annotations
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38
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5 # provided as GFF / GTF files by selecting on:
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40
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6 # - Priorty (defined by the order in the file)
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7 # - Provider
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8 # - dbkey (reference genome id)
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9 #
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10 # The gene_sets.loc file syntax is:
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11 # <name/UID> <dbkey> <path> <provider> <URL/reference*>
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12 # *optional
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38
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13 #
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14 # Please ensure maximally one TAB (\t) between two columns!
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15 # ---------------------------------------------------------
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16 #
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17 # In case you have TWO or MORE providers PER dbkey, the one mentioned
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18 # first in the file, should have the "default" priority.
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19 #
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20
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21
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22
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23 # [UCSC - UCSC Genes: knownGene]
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24
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25 #hg19.UCSC knownGene (mm/'yy) hg19 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf ucsc http://genome.ucsc.edu/
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26 #hg18.UCSC knownGene (mm/'yy) hg18 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf ucsc http://genome.ucsc.edu/
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27
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28
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29
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30 # [RefSeq Genes: RefGene]
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31 # link: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/
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32
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33
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34
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35 # [ Ensembl]
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36 # link: http://www.ensembl.org/info/data/ftp/index.html
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37
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38 #Homo_sapiens.GRCh37.74 hg19 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf ensembl ftp://ftp.ensembl.org/pub/release-74/gtf/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.gz
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39 #Homo_sapiens.NCBI36.54 hg18 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf ensembl ftp://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/Homo_sapiens.NCBI36.54.gtf.gz
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