# HG changeset patch
# User jjohnson
# Date 1410888924 14400
# Node ID 20453b6569072056ccae844cecf89d0b3093ffed
Imported from capsule None
diff -r 000000000000 -r 20453b656907 beta_basic.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/beta_basic.xml Tue Sep 16 13:35:24 2014 -0400
@@ -0,0 +1,188 @@
+
+ Predict the factors (TFs or CRs) direct target genes by combining the binding and expression data
+
+ beta_macros.xml
+
+
+
+ BETA basic
+ #include source=$common_opts#
+ #include source=$genome_opts#
+ #include source=$extended_opts#
+ &> $log
+
+
+
+
+
+
+
+
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+
+
+** BETA basic **
+
+@EXTERNAL_DOCUMENTATION@
+
+@CITATION_SECTION@
+
+This tool annotates the given intervals and scores with genome
+features such as gene body. It's the major module in CEAS package
+which is written by Hyunjin Gene Shin, published in Bioinformatics
+(pubmed id:19689956).
+
+.. class:: warningmark
+
+**NEED IMPROVEMENT**
+
+-----
+
+**Parameters**
+
+- **PEAKFILE file** contains peaks for the experiment in a bed
+ format file. Normally, it's produced by the peak calling tool. It's
+ required.
+- **EXPREFILE file** contains the differentially expressed genes in a tab
+ delimited text file. It's required.
+- **Kind** The kind of your expression file format, LIM for LIMMA standard
+ output with Microarray, CUF for Cuffdiffs standard output with RNA-seq,
+ BSF for BETA specific format, and O for other formats.
+- **genome** hg19 for human and mm9 for mouse. Others, don't set this parameter.
+- **gname2** If this switch is on, gene or transcript IDs in files given
+ through -e will be considered as official gene symbols, DEFAULT=FALSE
+- **EXPREINFO** is the columns info of the geneID, up/down status and statistcal
+ values column of your expression data,NOTE: use a comma as an connector.
+ for example: 2,5,7 means geneID in the 2nd column, Tscore in 5th column
+ and FDR in 7 column.
+- **REFERENCE** is the refgene info file downloaded from UCSC genome browser.
+ It is a tab delimited text file with gene annotation with refseq and gene symbol.
+ Input this file only if your genome is neither hg19 nor mm9.
+ profiling
+- **OUTPUT** to specify the output files directory
+- **bl** Whether or not to use CTCF boundary file to get the contributed peaks
+- **BOUNDARYFILE** is the file with reasonable boundaries if --bl is on and genome
+ is neither hg19 nor mm9.
+- **NAME** specify the name of the output files.
+- **DISTANCE** specify the distance wich peaks within it will be considered.
+- **DIFF_FDR** specify the differential genes by the 3rd column in file input
+ via -e, genes with less than this value will be considered as the differentially
+ changed genes.
+- **DIFF_AMOUNT** specify the differential genes the top #(DIFF_AMOUNT) ranked by
+ the 3rd column in file input via -e, genes ranked in the top # will be considered
+ as the differentially expressed genes.
+- **CUTOFF** specify a cutoff of ks-test in the function prediction part
+
+-----
+
+**Script parameter list of BETA basic**
+
+::
+
+ -h, --help show this help message and exit
+ -p PEAKFILE, --peakfile PEAKFILE
+ The bed format of peaks binding sites. (BETA support 3
+ or 5 columns bed format, CHROM, START, END (NAME,
+ SCORE))
+ -e EXPREFILE, --diff_expr EXPREFILE
+ The differential expression file get from limma for
+ MicroArray ddata and cuffdiff for RNAseq data
+ -k {LIM,CUF,BSF,O}, --kind {LIM,CUF,BSF,O}
+ The kind of your expression file,this is required,it
+ can be LIM, CUF, BSF, O. LIM for LIMMA standard
+ format. CUF for CUFDIFF standard format, BSF for BETA
+ specific format and O for other formats, if is 'O',
+ columns infor required via --info
+ -g {hg19,mm9}, --genome {hg19,mm9}
+ Specify your species, hg19, mm9. For other genome
+ assembily versions of human and mouse or other
+ species, ignore this parameter.
+ --gname2 If this switch is on, gene or transcript IDs in files
+ given through -e will be considered as official gene
+ symbols, DEFAULT=FALSE
+ --info EXPREINFO Specify the geneID, up/down status and statistcal
+ values column of your expression data,NOTE: use a
+ comma as an connector. for example: 2,5,7 means geneID
+ in the 2nd column, Tscore in 5th column and FDR in 7
+ column DEFAULT:2,5,7 for LIMMA; 2,10,13 for Cuffdiff
+ and 1,2,3 for BETA specific format
+ -r REFERENCE, --reference REFERENCE
+ The refgene info file downloaded from UCSC genome
+ browser.input this file only if your genome is neither
+ hg19 nor mm9
+ -o OUTPUT, --output OUTPUT
+ The directory to store all the output files, if you
+ don't set this, files will be output into the current
+ directory
+ --bl Whether or not use CTCF boundary to filter peaks
+ around a gene, DEFAULT=FALSE
+ --bf BOUNDARYFILE CTCF conserved peaks bed file, use this only when you
+ set --bl and the genome is neither hg19 nor mm9
+ --pn PEAKNUMBER The number of peaks you want to consider,
+ DEFAULT=10000
+ --method {score,distance}
+ Define the method to do the TF/CR function prediction,
+ score for regulatory potential, distance for the
+ distance to the proximal binding peak. DEFAULT:SCORE
+ -n NAME, --name NAME This argument is used to name the result file.If not
+ set, the peakfile name will be used instead
+ -d DISTANCE, --distance DISTANCE
+ Set a number which unit is 'base'. It will get peaks
+ within this distance from gene TSS. default:100000
+ (100kb)
+ --df DIFF_FDR Input a number 0~1 as a threshold to pick out the most
+ significant differential expressed genes by FDR,
+ DEFAULT = 1, that is select all the genes
+ --da DIFF_AMOUNT Get the most significant differential expressed genes
+ by the percentage(0-1) or number(larger than 1)Input a
+ number between 0-1, the rank based on fdr for example,
+ 2000, so that the script will only consider top 2000
+ genes as the differentially expressed genes. DEFAULT =
+ 0.5, that is select top 50 percent genes of up and
+ down seprately. NOTE: if you want to use diff_fdr,
+ please set this parameter to 1, otherwise it will get
+ the intersection of these two parameters
+ -c CUTOFF, --cutoff CUTOFF
+ Input a number between 0~1 as a threshold to select
+ the closer target gene list(up regulate or down
+ regulate or both) with the p value was called by one
+ side ks-test, DEFAULT = 0.001
+
+
+
+
diff -r 000000000000 -r 20453b656907 beta_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/beta_macros.xml Tue Sep 16 13:35:24 2014 -0400
@@ -0,0 +1,185 @@
+
+
+
+
+ numpy
+ R
+ beta
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+ ^\d+,\d+,\d+$
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+
+ -p "$peakfile"
+ -d $distance --pn $peaknumber -o $output_dir -n $name
+
+
+
+#if $refGenome.genomeName == 'hg19':
+ -g $refGenome.genomeName
+ ## -r \$BETA_LIB_PATH/BETA/references/hg19.refseq
+ #if $refGenome.boundary.boundaryLimit:
+ --bl
+ ## --bf \$BETA_LIB_PATH/BETA/references/hg19_CTCF_bound.bed
+ #end if
+#elif $refGenome.genomeName == 'mm9':
+ -g $refGenome.genomeName
+ ## -r \$BETA_LIB_PATH/BETA/references/mm9.refseq
+ #if $refGenome.boundary.boundaryLimit:
+ --bl
+ ## --bf \$BETA_LIB_PATH/BETA/references/mm9_CTCF_bound.bed
+ #end if
+#else
+ -r $refGenome.refseq
+ #if $refGenome.boundary.boundaryLimit:
+ --bl
+ --bf $refGenome.boundary.bl_bed
+ #end if
+#end if
+
+
+#if $refGenomeSource.genomeSource == 'cached':
+ --gs $refGenomeSource.all_fasta_source.fields.path
+#else
+ --gs $refGenomeSource.ownFile
+#end if
+
+
+
+ -e "$exprefile"
+ -k $expression.kind --info $expression.expreinfo --method $method
+ --da $diff_amount --df $diff_fdr -c 1
+#if $gname2 == "Gene_Symbol":
+ --gname2"
+#end if
+
+
+
+
+For details about this application, please go to:
+ http://cistrome.org/BETA/index.html
+
+
+ ------
+
+**Citation**
+
+For the underlying tool, please cite the following publication:
+Wang, S., Sun, H., Ma, J., Zang, C., Wang, C., Wang, J., Tang Q, Meyer CA, Zhang Y, Liu, X. S. (2013). Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nature protocols, 8(12), 2502-2515.
+PMID: 24263090
+
+
+
diff -r 000000000000 -r 20453b656907 beta_minus.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/beta_minus.xml Tue Sep 16 13:35:24 2014 -0400
@@ -0,0 +1,111 @@
+
+ Predict the factors (TFs or CRs) direct target genes by only binding data
+
+ beta_macros.xml
+
+
+
+ BETA minus
+ #include source=$common_opts#
+ #include source=$genome_opts#
+ &> $log
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+** BETA minus **
+
+@EXTERNAL_DOCUMENTATION@
+
+@CITATION_SECTION@
+
+This tool annotates the given intervals and scores with genome
+features such as gene body. It's the major module in CEAS package
+which is written by Hyunjin Gene Shin, published in Bioinformatics
+(pubmed id:19689956).
+
+.. class:: warningmark
+
+**NEED IMPROVEMENT**
+
+-----
+
+**Parameters**
+
+- **PEAKFILE file** contains peaks for the experiment in a bed
+ format file. Normally, it's produced by the peak calling tool. It's
+ required.
+- **genome** hg19 for human and mm9 for mouse. Others, don't set this parameter.
+- **REFERENCE** is the refgene info file downloaded from UCSC genome browser.
+ It is a tab delimited text file with gene annotation with refseq and gene symbol.
+ Input this file only if your genome is neither hg19 nor mm9.
+ profiling
+- **OUTPUT** to specify the output files directory
+- **bl** Whether or not to use CTCF boundary file to get the contributed peaks
+- **NAME** specify the name of the output files.
+- **DISTANCE** specify the distance wich peaks within it will be considered.
+
+
+-----
+
+**script parameter list of BETA minus**
+
+::
+
+ -h, --help show this help message and exit
+ -p PEAKFILE, --peakfile PEAKFILE
+ The bed format of peaks binding sites.
+ BETA supports 3 or 5 columns bed format: CHROM, START, END [NAME, SCORE]
+ -g {hg19,mm9}, --genome {hg19,mm9}
+ Specify your species, {hg19, mm9}
+ -r REFERENCE, --reference REFERENCE
+ the refgene info file downloaded from UCSC genome
+ browser.input this file only if your genome is neither
+ hg19 nor mm9
+ -o OUTPUT, --output OUTPUT
+ the directory to store all the output files, if you
+ don't set this, files will be output into the current
+ directory
+ --bl whether or not use CTCF boundary to filter peaks
+ around a gene, DEFAULT=FALSE
+ --pn PEAKNUMBER the number of peaks you want to consider, DEFAULT=10000
+ -n NAME, --name NAME this argument is used to name the result file.If not
+ set, the peakfile name will be used instead
+ -d DISTANCE, --distance DISTANCE
+ Set a number which unit is 'base'. It will get peaks
+ within this distance from gene TSS. default:100000 (100kb)
+
+
+
+
diff -r 000000000000 -r 20453b656907 beta_plus.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/beta_plus.xml Tue Sep 16 13:35:24 2014 -0400
@@ -0,0 +1,215 @@
+
+ Predict the factors (TFs or CRs) direct target genes by combining the binding and expression data, then do motif analysis on target regions
+
+ beta_macros.xml
+
+
+
+ BETA plus
+ #include source=$common_opts#
+ #include source=$genome_opts#
+ #include source=$ref_genome_seq_opts#
+ #include source=$extended_opts#
+ --mn $motifs
+ &> $log &&
+ mkdir -p $motifresult.extra_files_path &&
+ cp BETA_OUTPUT/motifresult/betamotif.html $motifresult &&
+ cp BETA_OUTPUT/motifresult/*.js $motifresult.extra_files_path &&
+ cp BETA_OUTPUT/motifresult/*.css $motifresult.extra_files_path &&
+ cp -r BETA_OUTPUT/motifresult/img $motifresult.extra_files_path
+
+
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+
+
+
+
+
+
+
+** BETA plus **
+
+@EXTERNAL_DOCUMENTATION@
+
+@CITATION_SECTION@
+
+This tool annotates the given intervals and scores with genome
+features such as gene body.
+Predicts Direct targets of TF and the active/repressive function
+prediction. Does motif analysis at targets region as well.
+It's the major module in CEAS package
+which is written by Hyunjin Gene Shin, published in Bioinformatics
+(pubmed id:19689956).
+
+.. class:: warningmark
+
+**NEED IMPROVEMENT**
+
+-----
+
+**Parameters**
+
+- **PEAKFILE file** contains peaks for the experiment in a bed
+ format file. Normally, it's produced by the peak calling tool. It's
+ required.
+- **EXPREFILE file** contains the differentially expressed genes in a tab
+ delimited text file. It's required.
+- **Kind** The kind of your expression file format, LIM for LIMMA standard
+ output with Microarray, CUF for Cuffdiffs standard output with RNA-seq,
+ BSF for BETA specific format, and O for other formats.
+- **genome** hg19 for human and mm9 for mouse. Others, don't set this parameter.
+- **genomereference** Genome reference data with fasta format
+- **gname2** If this switch is on, gene or transcript IDs in files given
+ through -e will be considered as official gene symbols, DEFAULT=FALSE
+- **EXPREINFO** is the columns info of the geneID, up/down status and statistcal
+ values column of your expression data,NOTE: use a comma as an connector.
+ for example: 2,5,7 means geneID in the 2nd column, Tscore in 5th column
+ and FDR in 7 column.
+- **REFERENCE** is the refgene info file downloaded from UCSC genome browser.
+ It is a tab delimited text file with gene annotation with refseq and gene symbol.
+ Input this file only if your genome is neither hg19 nor mm9.
+ profiling
+- **OUTPUT** to specify the output files directory
+- **bl** Whether or not to use CTCF boundary file to get the contributed peaks
+- **BOUNDARYFILE** is the file with reasonable boundaries if --bl is on and genome
+ is neither hg19 nor mm9.
+- **NAME** specify the name of the output files.
+- **DISTANCE** specify the distance wich peaks within it will be considered.
+- **DIFF_FDR** specify the differential genes by the 3rd column in file input
+ via -e, genes with less than this value will be considered as the differentially
+ changed genes.
+- **DIFF_AMOUNT** specify the differential genes the top #(DIFF_AMOUNT) ranked by
+ the 3rd column in file input via -e, genes ranked in the top # will be considered
+ as the differentially expressed genes.
+- **CUTOFF** specify a cutoff of ks-test in the function prediction part
+
+
+-----
+
+**Script parameter list of BETA plus**
+
+::
+
+ -h, --help show this help message and exit
+ -p PEAKFILE, --peakfile PEAKFILE
+ The bed format of peaks binding sites. (BETA support 3
+ or 5 columns bed format, CHROM, START, END (NAME,
+ SCORE))
+ -e EXPREFILE, --diff_expr EXPREFILE
+ The differential expression file get from limma for
+ MicroArray ddata and cuffdiff for RNAseq data
+ -k {LIM,CUF,BSF,O}, --kind {LIM,CUF,BSF,O}
+ The kind of your expression file,this is required,it
+ can be LIM, CUF, BSF, O. LIM for LIMMA standard
+ format. CUF for CUFDIFF standard format, BSF for BETA
+ specific format and O for other formats, if is 'O',
+ columns infor required via --info
+ -g {hg19,mm9}, --genome {hg19,mm9}
+ Specify your species, hg19, mm9
+ --gs GENOMEREFERNCE GenomeReference file with fasta format
+ --gname2 If this switch is on, gene or transcript IDs in files
+ given through -e will be considered as official gene
+ symbols, DEFAULT=FALSE
+ --info EXPREINFO Specify the geneID, up/down status and statistcal
+ values column of your expression data,NOTE: use a
+ comma as an connector. for example: 2,5,7 means geneID
+ in the 2nd column, Tscore in 5th column and FDR in 7
+ column DEFAULT:2,5,7 for LIMMA; 2,10,13 for Cuffdiff
+ and 1,2,3 for BETA specific format
+ -r REFERENCE, --reference REFERENCE
+ The refgene info file downloaded from UCSC genome
+ browser.input this file only if your genome is neither
+ hg19 nor mm9
+ -o OUTPUT, --output OUTPUT
+ The directory to store all the output files, if you
+ don't set this, files will be output into the current
+ directory
+ --bl Whether or not use CTCF boundary to filter peaks
+ around a gene, DEFAULT=FALSE
+ --bf BOUNDARYFILE CTCF conserved peaks bed file, use this only when you
+ set --bl and the genome is neither hg19 nor mm9
+ --pn PEAKNUMBER The number of peaks you want to consider,
+ DEFAULT=10000
+ --method {score,distance}
+ Define the method to do the TF/CR function prediction,
+ score for regulatory potential, distance for the
+ distance to the proximal binding peak. DEFAULT:SCORE
+ -n NAME, --name NAME This argument is used to name the result file.If not
+ set, the peakfile name will be used instead
+ -d DISTANCE, --distance DISTANCE
+ Set a number which unit is 'base'. It will get peaks
+ within this distance from gene TSS. default:100000
+ (100kb)
+ --df DIFF_FDR Input a number 0~1 as a threshold to pick out the most
+ significant differential expressed genes by FDR,
+ DEFAULT = 1, that is select all the genes
+ --da DIFF_AMOUNT Get the most significant differential expressed genes
+ by the percentage(0-1) or number(larger than 1)Input a
+ number between 0-1, the rank based on fdr for example,
+ 2000, so that the script will only consider top 2000
+ genes as the differentially expressed genes. DEFAULT =
+ 0.5, that is select top 50 percent genes of up and
+ down seprately. NOTE: if you want to use diff_fdr,
+ please set this parameter to 1, otherwise it will get
+ the intersection of these two parameters
+ -c CUTOFF, --cutoff CUTOFF
+ Input a number between 0~1 as a threshold to select
+ the closer target gene list(up regulate or down
+ regulate or both) with the p value was called by one
+ side ks-test, DEFAULT = 0.001
+
+
+
diff -r 000000000000 -r 20453b656907 test-data/diff_expr.xls
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/diff_expr.xls Tue Sep 16 13:35:24 2014 -0400
@@ -0,0 +1,481 @@
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+"15808" "NM_005551_at" 3.21455049282016 9.16992988250215 35.3250580701301 8.07078113559923e-11 4.17993094276913e-07 14.0522721119642
+"32946" "NR_045763_at" 3.21455049282016 9.16992988250215 35.3250580701301 8.07078113559923e-11 4.17993094276913e-07 14.0522721119642
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+"11959" "NM_001280_at" -0.313565624928774 11.5517677095165 -5.87746833096408 0.000253164723860419 0.0080677394457016 0.590604854547801
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+"20043" "NM_017509_at" 0.302316510055042 5.69304104204907 4.23566930620546 0.00228131817788978 0.0330938286987348 -1.7227636466034
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+"25580" "NM_138392_at" -0.203652535744714 6.96144726252987 -3.96823163968539 0.00338570869341308 0.0423322881433596 -2.13529072506085
+"16442" "NM_006270_at" 0.210978626036527 7.85003492224526 3.70334199100026 0.00505486284038159 0.0541740881159761 -2.55228349353791
+"13339" "NM_002812_at" 0.310403681648889 10.8802723443825 3.68186149548619 0.00522397766895206 0.0553167185789793 -2.58642895159612
+"14710" "NM_004343_at" 0.203410720903316 10.8592065507189 3.50731820340997 0.00684021080283789 0.0661056025439772 -2.8655115279896
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+"15126" "NM_004793_at" -0.299768296398 9.50435296587981 -3.45405245658428 0.00743218189793424 0.0692858537078163 -2.95120965680756
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diff -r 000000000000 -r 20453b656907 test-data/peaks.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peaks.bed Tue Sep 16 13:35:24 2014 -0400
@@ -0,0 +1,72 @@
+chr19 518572 519514 AR_LNCaP_4717 59.19
+chr19 1020702 1021980 AR_LNCaP_4725 388.32
+chr19 1094875 1095946 AR_LNCaP_4726 63.11
+chr19 1228829 1229967 AR_LNCaP_4728 54.26
+chr19 1382835 1384282 AR_LNCaP_4733 231.69
+chr19 2269491 2270735 AR_LNCaP_4741 60.70
+chr19 2543491 2544716 AR_LNCaP_4747 228.53
+chr19 3185501 3186253 AR_LNCaP_4748 52.27
+chr19 3336410 3337572 AR_LNCaP_4750 94.92
+chr19 4723422 4724314 AR_LNCaP_4753 74.30
+chr19 4724416 4725364 AR_LNCaP_4754 115.50
+chr19 5268577 5269878 AR_LNCaP_4755 290.97
+chr19 5620739 5621928 AR_LNCaP_4756 70.46
+chr19 7489621 7490513 AR_LNCaP_4760 73.95
+chr19 8372986 8374008 AR_LNCaP_4765 76.91
+chr19 10875668 10876743 AR_LNCaP_4773 72.61
+chr19 12721199 12722240 AR_LNCaP_4774 61.84
+chr19 13101849 13102755 AR_LNCaP_4777 291.05
+chr19 13318039 13318869 AR_LNCaP_4783 52.65
+chr19 13875326 13876277 AR_LNCaP_4785 51.19
+chr19 14583973 14585287 AR_LNCaP_4788 88.28
+chr19 15414587 15415713 AR_LNCaP_4789 76.29
+chr19 15489711 15490727 AR_LNCaP_4790 59.97
+chr19 16473642 16474670 AR_LNCaP_4793 70.70
+chr19 16973078 16974032 AR_LNCaP_4796 76.09
+chr19 17096748 17097899 AR_LNCaP_4797 62.09
+chr19 17345963 17347135 AR_LNCaP_4798 92.15
+chr19 18391901 18392804 AR_LNCaP_4802 51.13
+chr19 18808279 18810382 AR_LNCaP_4809 149.25
+chr19 28392798 28393702 AR_LNCaP_4818 54.45
+chr19 28426028 28427157 AR_LNCaP_4820 51.30
+chr19 28431530 28432644 AR_LNCaP_4821 63.20
+chr19 28607592 28608803 AR_LNCaP_4822 101.52
+chr19 30020337 30021328 AR_LNCaP_4827 52.78
+chr19 30211394 30212475 AR_LNCaP_4829 53.76
+chr19 30551328 30552172 AR_LNCaP_4830 52.34
+chr19 30643279 30644356 AR_LNCaP_4831 229.66
+chr19 30932770 30934129 AR_LNCaP_4833 103.59
+chr19 32210230 32211210 AR_LNCaP_4839 59.08
+chr19 32234483 32235456 AR_LNCaP_4840 51.81
+chr19 33667285 33668666 AR_LNCaP_4846 438.19
+chr19 33863966 33865008 AR_LNCaP_4847 54.29
+chr19 34663548 34664231 AR_LNCaP_4849 50.15
+chr19 34800905 34802101 AR_LNCaP_4852 292.94
+chr19 34817831 34818944 AR_LNCaP_4853 124.21
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+chr19 34962763 34963890 AR_LNCaP_4855 95.70
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+chr19 38789237 38790370 AR_LNCaP_4861 76.81
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+chr19 39902325 39903668 AR_LNCaP_4869 84.54
+chr19 41139890 41140917 AR_LNCaP_4873 50.16
+chr19 42502780 42503773 AR_LNCaP_4877 62.07
+chr19 44198615 44199741 AR_LNCaP_4880 120.50
+chr19 45595987 45596898 AR_LNCaP_4882 51.31
+chr19 45655043 45656039 AR_LNCaP_4883 58.06
+chr19 45981823 45982582 AR_LNCaP_4886 52.62
+chr19 46246031 46247043 AR_LNCaP_4887 420.28
+chr19 47290422 47291287 AR_LNCaP_4892 51.42
+chr19 47470793 47471707 AR_LNCaP_4893 53.30
+chr19 47950633 47951639 AR_LNCaP_4896 60.92
+chr19 48204625 48205733 AR_LNCaP_4900 71.83
+chr19 50154344 50155915 AR_LNCaP_4912 84.12
+chr19 51354060 51354999 AR_LNCaP_4914 62.11
+chr19 51372841 51373704 AR_LNCaP_4915 50.33
+chr19 51392207 51393248 AR_LNCaP_4916 132.09
+chr19 55592961 55594092 AR_LNCaP_4921 68.33
+chr19 57639841 57640962 AR_LNCaP_4929 105.02
+chr19 57723651 57724464 AR_LNCaP_4931 57.62
+chr19 57873567 57875214 AR_LNCaP_4932 131.57
+chr19 58919368 58920359 AR_LNCaP_4940 58.81
diff -r 000000000000 -r 20453b656907 tool-data/all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample Tue Sep 16 13:35:24 2014 -0400
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
diff -r 000000000000 -r 20453b656907 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue Sep 16 13:35:24 2014 -0400
@@ -0,0 +1,7 @@
+
+
+
+ value, dbkey, name, path
+
+
+
diff -r 000000000000 -r 20453b656907 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Sep 16 13:35:24 2014 -0400
@@ -0,0 +1,12 @@
+
+
+
+
+
+
+
+
+
+
+
+