Mercurial > repos > jjohnson > defuse
annotate tool-data/defuse.loc.sample @ 9:9f30de0ff090 draft
Add gmap_setup_bin and gmap_index_directory to defuse.xml config file generation
| author | Jim Johnson <jj@umn.edu> |
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| date | Mon, 14 Jan 2013 11:26:17 -0600 |
| parents | 679a5c7b1294 |
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679a5c7b1294
deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
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1 ## Configurstion info for prepared data references for DeFuse |
| 1 | 2 ## http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2 |
| 3 ## 3 columns separated by the TAB character | |
| 4 ## The 3rd column has dictionary values that will be substituted in the config file for defuse | |
| 5 ## It should likely contain keys: dataset_directory gene_models genome_fasta repeats_filename est_fasta est_alignments unigene_fasta | |
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679a5c7b1294
deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
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6 ## If this is not a Homo_sapiens reference also need keys: gene_id_pattern transcript_id_pattern chromosomes |
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679a5c7b1294
deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
7 |
| 1 | 8 #db_key name {'config_key':'config_value'} |
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679a5c7b1294
deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
9 #hg19 GRCh37(hg19) {'gene_id_pattern':'ENSG\d+', 'transcript_id_pattern':'ENST\d+', 'dataset_directory':'/data/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'} |
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679a5c7b1294
deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
10 #mm9 NCBIM37(mm9) {'gene_id_pattern':'ENSMUSG\d+', 'transcript_id_pattern':'ENSMUST\d+', 'dataset_directory':'/data/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'} |
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679a5c7b1294
deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
11 #mm8 NCBIM36(mm8) {'gene_id_pattern':'ENSMUSG\d+', 'transcript_id_pattern':'ENSMUST\d+', 'dataset_directory':'/data/genomes/Mmusculus/mm9/defuse', 'gene_models':'$(dataset_directory)/Mus_musculus.NCBIM36.46.gtf', 'genome_fasta':'$(dataset_directory)/Mus_musculus.NCBIM36.46.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', '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'} |