Mercurial > repos > jjohnson > defuse
changeset 2:4245c2b047de
Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 08 Nov 2011 13:56:35 -0600 |
| parents | 36306d8086fa |
| children | c90022a13c7c |
| files | README defuse-0.4.2.tar.gz defuse-0.4.3.tar.gz defuse.xml modified_scripts.tgz tool-data/defuse.loc.sample |
| diffstat | 6 files changed, 34 insertions(+), 40 deletions(-) [+] |
line wrap: on
line diff
--- a/README Fri Sep 16 12:41:37 2011 -0500 +++ b/README Tue Nov 08 13:56:35 2011 -0600 @@ -1,33 +1,29 @@ -The DeFuse galaxy tool is based on DeFuse_Version_0.4.2 +The DeFuse galaxy tool is based on DeFuse_Version_0.4.3 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page DeFuse is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to reduce the number of false positives and produces a fully annotated output for each predicted fusion. Manual: - http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2 + http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.3 -The included defuse source code is from: http://sourceforge.net/projects/defuse/files/defuse/0.4/defuse-0.4.2.tar.gz/download -(without the defuse-0.4.2 dir level) -tar zxf defuse-0.4.2.tar.gz -cd tool +The included defuse source code is from: http://sourceforge.net/projects/defuse/files/defuse/0.4/defuse-0.4.3.tar.gz/download +(to install uncompress the defuse source and navigate to the tools dir and type make) +tar zxf defuse-0.4.3.tar.gz +cd defuse-0.4.3/tool make -cd .. +cd ../.. -To use with non human genome references: -tar zxf modified_scripts.tgz -Defuse source was modified to include 2 extra parameters for non human references: gene_id_pattern and transcript_id_pattern - scripts/alignjob.pl - scripts/annotate_fusions.pl - scripts/calculate_expression_simple.pl - scripts/filter_bulk_fusion_reads.pl - scripts/filter_sam_genes.pl - scripts/find_concordant_ensembl.pl - scripts/find_gene_clusters.pl +Generate Reference Datasets as described in the Manual: + + The manual has detailed instructions on how to set up reference datasets for Human hg19 and hg18. + We were able to follow the same basic procedures to set up a reference for Mouse mm9. + + These datasets should be referenced in the tool-data/defuse.loc file. The defuse.xml galaxy tool wrapper will generate a defuse config.txt using values from tool-data/defuse.loc -and call scripts/defuse.pl +and call defuse-0.4.3/scripts/defuse.pl
--- a/defuse.xml Fri Sep 16 12:41:37 2011 -0500 +++ b/defuse.xml Tue Nov 08 13:56:35 2011 -0600 @@ -1,10 +1,14 @@ -<tool id="defuse" name="DeFuse" version="1.0"> +<tool id="defuse" name="DeFuse" version="1.1"> <description>identify fusion transcripts</description> <requirements> <requirement type="binary"></requirement> </requirements> <command interpreter="perl"> - scripts/defuse.pl + ## Find the defuse.pl in the galaxy tool path + #import Cheetah.FileUtils + #set $toolpath = '/'.join([$__root_dir__,'tools','defuse']) + #set $defuse = $Cheetah.FileUtils.findFiles($toolpath,['defuse.pl'],[],['tools','external','include','em','data'])[0] + $defuse -c `cp $defuse_config $config_txt; echo $defuse_config` -d `mkdir -p data_dir; ln -s $left_pairendreads data_dir/reads_1.fastq; ln -s $right_pairendreads data_dir/reads_2.fastq; echo data_dir` -o output_dir -p 8 @@ -86,20 +90,7 @@ # # At a minimum, change all values enclused by [] # -# Gene/Transcript id pattern -gene_id_pattern = #slurp -#try -$ref_dict['gene_id_pattern'] -transcript_id_pattern = #slurp -#except -ENSG\d+ -#end try -#try -$ref_dict['transcript_id_pattern'] -#except -ENST\d+ -#end try - + # Directory where the defuse code was unpacked ## Default location in the tool/defuse directory # source_directory = ${__root_dir__}/tools/defuse @@ -107,7 +98,15 @@ #try $ref_dict['source_directory'] #except -${__root_dir__}/tools/defuse +#try +## Try to find the defuse source dir in the galaxy tool path +#import Cheetah.FileUtils +#set $toolpath = '/'.join([$__root_dir__,'tools','defuse']) +#set $defuse = $Cheetah.FileUtils.findFiles($toolpath,['defuse.pl'],[],['tools','external','include','em','data'])[0] +$defuse.replace('/scripts/defuse.pl','') +#except +${__root_dir__}/tools/defuse/defuse +#end try #end try # Directory where you want your dataset
--- a/tool-data/defuse.loc.sample Fri Sep 16 12:41:37 2011 -0500 +++ b/tool-data/defuse.loc.sample Tue Nov 08 13:56:35 2011 -0600 @@ -1,10 +1,9 @@ -## Configurstion info for prepared data references for DeFuse +## 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 -## If this is not a Homo_sapiens reference also need keys: gene_id_pattern transcript_id_pattern chromosomes - #db_key name {'config_key':'config_value'} -hg19 GRCh37(hg19) {'samtools_bin':'/soft/samtools/0.1.12a/bin/samtools', 'gene_id_pattern':'ENSG\d+', 'transcript_id_pattern':'ENST\d+', '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/0.1.12a/bin/samtools', 'gene_id_pattern':'ENSMUSG\d+', 'transcript_id_pattern':'ENSMUST\d+', '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'} +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'}