Mercurial > repos > yhoogstrate > featurecounts_valid_gff
changeset 38:ef6984098204
Uploaded
| author | yhoogstrate |
|---|---|
| date | Fri, 21 Feb 2014 04:22:25 -0500 |
| parents | bdd5f2ecd087 |
| children | 0abd1de08703 |
| files | gene_sets.loc.sample tool-data/gene_sets.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 41 insertions(+), 34 deletions(-) [+] |
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--- a/gene_sets.loc.sample Mon Feb 17 10:49:18 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ -# Because of this file, galaxy tools can access gene annotations -# provided as GFF / GTF files by selecting on: -# - Priorty (order in the file) -# - Provider -# - dbkey (reference genome id) -# -# The gene_sets.loc file syntax is: -# <name/UID> <dbkey> <path> <provider> <URL/reference*> -# -# *optional -# -# In case you have TWO or MORE providers PER dbkey, the one mentioned -# first in the file, should have the "default" priority. -# - - - -# [UCSC - UCSC Genes: knownGene] - -#hg19.UCSC knownGene (mm/'yy) hg19 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf ucsc http://genome.ucsc.edu/ -#hg18.UCSC knownGene (mm/'yy) hg18 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf ucsc http://genome.ucsc.edu/ - - - -# [RefSeq Genes: RefGene] -# link: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/ - - - -# [ Ensembl] -# link: http://www.ensembl.org/info/data/ftp/index.html - -#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 -#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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/gene_sets.loc.sample Fri Feb 21 04:22:25 2014 -0500 @@ -0,0 +1,36 @@ +# Because of this file, galaxy tools can access gene annotations +# provided as GFF / GTF files by selecting on: +# - Priorty (order in the file) +# - Provider +# - dbkey (reference genome id) +# +# The gene_sets.loc file syntax is: +# <name/UID> <dbkey> <path> <provider> <URL/reference*> +# +# *optional +# +# Please ensure maximally one TAB per column! +# +# In case you have TWO or MORE providers PER dbkey, the one mentioned +# first in the file, should have the "default" priority. +# + + + +# [UCSC - UCSC Genes: knownGene] + +#hg19.UCSC knownGene (mm/'yy) hg19 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf ucsc http://genome.ucsc.edu/ +#hg18.UCSC knownGene (mm/'yy) hg18 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf ucsc http://genome.ucsc.edu/ + + + +# [RefSeq Genes: RefGene] +# link: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/ + + + +# [ Ensembl] +# link: http://www.ensembl.org/info/data/ftp/index.html + +#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 +#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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Feb 21 04:22:25 2014 -0500 @@ -0,0 +1,5 @@ +<?xml version="1.0"?> +<table name="gene_sets" comment_char="#"> + <columns>name, dbkey, value, provider, reference</columns> + <file path="tool-data/gene_sets.loc.sample" /> +</table> \ No newline at end of file