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DeFuse - Allow user to save the workspace, create an html file with links to the files in the workspace. Allow the creatation of an HTML formatted results.filtered.tsv with links to cluster detail provided by the get_read.pl command.
author Jim Johnson <jj@umn.edu>
date Fri, 06 Jan 2012 16:06:17 -0600
parents 4245c2b047de
children 679a5c7b1294
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4245c2b047de Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
parents: 1
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1 ## Configurstion info for prepared data references for DeFuse Version 0.4.3
4245c2b047de Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
parents: 1
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2 # http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
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36306d8086fa Remove defuse dir
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3 ## http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
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4 ## 3 columns separated by the TAB character
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
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5 ## The 3rd column has dictionary values that will be substituted in the config file for defuse
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
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6 ## It should likely contain keys: dataset_directory gene_models genome_fasta repeats_filename est_fasta est_alignments unigene_fasta
36306d8086fa Remove defuse dir
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7 #db_key name {'config_key':'config_value'}
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4245c2b047de Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
parents: 1
diff changeset
8 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'}
4245c2b047de Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
parents: 1
diff changeset
9 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'}