--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/defuse.loc.sample	Thu Nov 10 09:56:05 2011 -0500
@@ -0,0 +1,9 @@
+## Configurstion info for prepared data references for DeFuse Version 0.4.3 
+#  http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
+## http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2
+## 3 columns separated by the TAB character
+## The 3rd column has dictionary values that will be substituted in the config file for defuse
+## It should likely contain keys:   dataset_directory gene_models genome_fasta repeats_filename est_fasta est_alignments unigene_fasta
+#db_key	name	{'config_key':'config_value'}
+hg19	GRCh37(hg19)	{'samtools_bin':'/soft/samtools/0.1.8/bin/samtools', 'dataset_directory':'/project/db/genomes/Hsapiens/hg19/defuse', 'gene_models':'$(dataset_directory)/Homo_sapiens.GRCh37.62.gtf', 'genome_fasta':'$(dataset_directory)/Homo_sapiens.GRCh37.62.dna.chromosome.fa', 'repeats_filename':'$(dataset_directory)/rmsk.txt', 'est_fasta':'$(dataset_directory)/est.fa', 'est_alignments':'$(dataset_directory)/intronEst.txt', 'unigene_fasta':'$(dataset_directory)/Hs.seq.uniq', '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,MT', 'mt_chromosome':'MT', 'gene_sources':'IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding', 'ig_gene_sources':'IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene', 'rrna_gene_sources':'Mt_rRNA,rRNA,rRNA_pseudogene'}
+mm9	NCBIM37(mm9)	{'samtools_bin':'/soft/samtools/0.1.8/bin/samtools', 'dataset_directory':'/project/db/genomes/Mmusculus/mm9/defuse', 'gene_models':'$(dataset_directory)/Mus_musculus.NCBIM37.63.gtf', 'genome_fasta':'$(dataset_directory)/Mus_musculus.NCBIM37.63.dna.chromosome.fa', 'repeats_filename':'$(dataset_directory)/rmsk.txt', 'est_fasta':'$(dataset_directory)/est.fa', 'est_alignments':'$(dataset_directory)/intronEst.txt', 'unigene_fasta':'$(dataset_directory)/Mm.seq.uniq', 'chromosomes':'1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y,MT', 'mt_chromosome':'MT', 'gene_sources':'IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding', 'ig_gene_sources':'IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene', 'rrna_gene_sources':'Mt_rRNA,rRNA,rRNA_pseudogene'}