|
0
|
1 # This is a sample file distributed with Galaxy that enables tools
|
|
|
2 # to use gene/exon annotations in the GFF/GTF format. You will need
|
|
|
3 # to add all the gene set annotations in this configuration file.
|
|
|
4 # Because of this file, galaxy tools are able to access gene annotations
|
|
|
5 # provided as GFF / GTF files by selecting on:
|
|
|
6 # - Priorty (defined by the order in the file)
|
|
|
7 # - Provider
|
|
|
8 # - dbkey (reference genome id)
|
|
|
9 #
|
|
|
10 # The gene_sets.loc file syntax is:
|
|
|
11 # <name/UID> <dbkey> <path> <provider> <URL/reference*>
|
|
|
12 # *optional
|
|
|
13 #
|
|
|
14 # Please ensure maximally one TAB (\t) between two columns!
|
|
|
15 # ---------------------------------------------------------
|
|
|
16 #
|
|
|
17 # In case you have TWO or MORE providers PER dbkey, the one mentioned
|
|
|
18 # first in the file, should have the "default" priority.
|
|
|
19 #
|
|
|
20
|
|
|
21
|
|
|
22
|
|
|
23 # [UCSC - UCSC Genes: knownGene]
|
|
|
24
|
|
|
25 #hg19.UCSC knownGene (mm/'yy) hg19 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf ucsc http://genome.ucsc.edu/
|
|
|
26 #hg18.UCSC knownGene (mm/'yy) hg18 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf ucsc http://genome.ucsc.edu/
|
|
|
27
|
|
|
28
|
|
|
29
|
|
|
30 # [RefSeq Genes: RefGene]
|
|
|
31 # link: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/
|
|
|
32
|
|
|
33
|
|
|
34
|
|
|
35 # [ Ensembl]
|
|
|
36 # link: http://www.ensembl.org/info/data/ftp/index.html
|
|
|
37
|
|
|
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
|
|
|
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
|
