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org_settings.cfg
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/
org_settings.cfg
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# This file is used by org_settings.py to return sets of paths/settings like
# genomic sequence files, genome sizes, etc. It is formatted according to
# Python's ConfigParser.CongifParser specification:
#
# http://docs.python.org/library/configparser.html
#
# Before installation, add any system-specific settings to the categories below,
# where categories correspond to organism/genome names, creating new category
# headings where desired.
#
# User-specific organisms and settings may be specified in:
#
# os.path.expanduser('~/.org_settings.cfg')
#
# with the same format. Settings in user configuration files override system-wide
# settings.
#
# A minimal organism configuration requires at least genome_dir and genome_size,
# other settings may be required for different tools (e.g. theme_* for THEME.py)
#
# field values can contain no spaces if they are to be exported to the command line
# (i.e. with org_settings.py)
[hg18]
description=UCSC hg18 (March '06 build) with full TRANSFAC hypothesis set
genome=hg18
genome_dir=/nfs/genomes/human_gp_mar_06
genome_size=2700000000
ucsc_chrom_sizes=%(genome_dir)s/%(genome)s.chrom.sizes
annotation_path=%(genome_dir)s/anno/refFlat-hg18-2010-08-17.txt
refgene_anno_path=%(genome_dir)s/anno/refFlat-hg18-2010-08-17.txt
known_gene_anno_path=%(genome_dir)s/anno/knownGene-hg18-2010-08-17.txt
known_gene_xref_path=%(genome_dir)s/anno/kgXref-hg18-2010-08-17.txt
theme_hypotheses=/nfs/vendata/cwng/TRANSFAC/2010_transfac_vert_all_filtic9.tamo
theme_markov=%(genome_dir)s/hg18_promoters_3000_1000.markov
[hg18clust]
description=UCSC hg18 (March '06 build) with clustered TRANSFAC hypothesis set
genome=hg18
genome=hg18
genome_dir=/nfs/genomes/human_gp_mar_06
genome_size=2700000000
ucsc_chrom_sizes=%(genome_dir)s/%(genome)s.chrom.sizes
annotation_path=%(genome_dir)s/anno/refFlat-hg18-2010-08-17.txt
refgene_anno_path=%(genome_dir)s/anno/refFlat-hg18-2010-08-17.txt
known_gene_anno_path=%(genome_dir)s/anno/knownGene-hg18-2010-08-17.txt
known_gene_xref_path=%(genome_dir)s/anno/kgXref-hg18-2010-08-17.txt
theme_hypotheses=/nfs/vendata/cwng/TRANSFAC/2010_transfac_vert_all_filtic9_sym_clus4.tamo
theme_markov=%(genome_dir)s/hg18_promoters_3000_1000.markov
weeder_freqfiles_path=%(genome_dir)s/weeder
[hg19]
description=UCSC hg19 (Feb '09 build) with full TRANSFAC hypothesis set
genome=hg19
genome_dir=/nfs/genomes/human_gp_feb_09
genome_size=2700000000
ucsc_chrom_sizes=%(genome_dir)s/%(genome)s.chrom.sizes
annotation_path=%(genome_dir)s/anno/refFlat-%(genome)s-2011-01-04.txt
refgene_anno_path=%(genome_dir)s/anno/refFlat-%(genome)s-2011-01-04.txt
known_gene_anno_path=%(genome_dir)s/anno/knownGene-%(genome)s-2011-01-04.txt
known_gene_xref_path=%(genome_dir)s/anno/kgXref-%(genome)s-2011-01-04.txt
theme_hypotheses=/nfs/vendata/cwng/TRANSFAC/2010_transfac_vert_all_filtic9.tamo
theme_markov=%(genome_dir)s/hg19_promoters_3000_1000.markov
[hg19clust]
description=UCSC hg19 (Feb '09 build) with clustered TRANSFAC hypothesis set
genome=hg19
genome_dir=/nfs/genomes/human_gp_feb_09
genome_size=2700000000
ucsc_chrom_sizes=%(genome_dir)s/%(genome)s.chrom.sizes
annotation_path=%(genome_dir)s/anno/refFlat-%(genome)s-2011-01-04.txt
refgene_anno_path=%(genome_dir)s/anno/refFlat-%(genome)s-2011-01-04.txt
known_gene_anno_path=%(genome_dir)s/anno/knownGene-%(genome)s-2011-01-04.txt
known_gene_xref_path=%(genome_dir)s/anno/kgXref-%(genome)s-2011-01-04.txt
theme_hypotheses=/nfs/vendata/cwng/TRANSFAC/2010_transfac_vert_all_filtic9_sym_clus4.tamo
theme_markov=%(genome_dir)s/hg19_promoters_3000_1000.markov
[mm9]
description=UCSC mm9 (July '07 build) with full TRANSFAC hypothesis set
genome=mm9
genome_dir=/nfs/genomes/mouse_gp_jul_07
genome_size=2107000000
ucsc_chrom_sizes=%(genome_dir)s/%(genome)s.chrom.sizes
annotation_path=%(genome_dir)s/anno/refFlat-%(genome)s.txt
refgene_anno_path=%(genome_dir)s/anno/refFlat-%(genome)s.txt
known_gene_anno_path=%(genome_dir)s/anno/knownGene-%(genome)s.txt
known_gene_xref_path=%(genome_dir)s/anno/kgXref-%(genome)s.txt
affy_to_known_path=%(genome_dir)s/anno/knownToMOE43-%(genome)s.txt
theme_hypotheses=/nfs/vendata/cwng/TRANSFAC/2010_transfac_vert_all_filtic9.tamo
theme_markov=/nfs/data/cwng/chipseq/hypotheses/Mouse.markov
[mm9clust]
description=UCSC mm9 (July '07 build) with clustered TRANSFAC hypothesis set
genome=mm9
genome_dir=/nfs/genomes/mouse_gp_jul_07
genome_size=2107000000
ucsc_chrom_sizes=%(genome_dir)s/%(genome)s.chrom.sizes
annotation_path=%(genome_dir)s/anno/refFlat-%(genome)s.txt
refgene_anno_path=%(genome_dir)s/anno/refFlat-%(genome)s.txt
known_gene_anno_path=%(genome_dir)s/anno/knownGene-%(genome)s.txt
known_gene_xref_path=%(genome_dir)s/anno/kgXref-%(genome)s.txt
affy_to_known_path=%(genome_dir)s/anno/knownToMOE430-%(genome)s.txt
theme_hypotheses=/nfs/vendata/cwng/TRANSFAC/2010_transfac_vert_all_filtic9_sym_clus4.tamo
theme_markov=/nfs/data/cwng/chipseq/hypotheses/Mouse.markov
[mm8]
description=UCSC mm8 (March '07 build) with full TRANSFAC hypothesis set
genome=mm8
genome_dir=/nfs/genomes/mouse_gp_mar_06
genome_size=2107000000
ucsc_chrom_sizes=%(genome_dir)s/%(genome)s.chrom.sizes
refgene_anno_path=%(genome_dir)s/anno/refFlat-2010-08-26.txt
annotation_path=%(refgene_anno_path)s
known_gene_anno_path=%(genome_dir)s/anno/knownGene-2010-08-26.txt
known_gene_xref_path=%(genome_dir)s/anno/kgXref-2010-08-26.txt
affy_to_known_path=%(genome_dir)s/anno/knownToMOE430-2010-08-26.txt
theme_hypotheses=/nfs/vendata/cwng/TRANSFAC/2010_transfac_vert_all_filtic9.tamo
theme_markov=/nfs/data/cwng/chipseq/hypotheses/Mouse.markov
# others...