# HG changeset patch # User kevyin # Date 1355955434 18000 # Node ID 4241b517de775a0e862f30344eb398b5bf677d0a # Parent 4b5b9c36ff6f8af937ed45f86ff654e33832bbb8 Deleted selected files diff -r 4b5b9c36ff6f -r 4241b517de77 README --- a/README Sun Dec 16 23:31:10 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -Homer wrapper for Galaxy - -Code repo: https://bitbucket.org/gvl/homer - -=========================================: -LICENSE for this wrapper: -=========================================: -Kevin Ying -Garvan Institute: http://www.garvan.org.au -GVL: https://genome.edu.au/wiki/GVL - -http://opensource.org/licenses/mit-license.php - diff -r 4b5b9c36ff6f -r 4241b517de77 annotatePeaks.xml --- a/annotatePeaks.xml Sun Dec 16 23:31:10 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ - - - homer - - - - - annotatePeaks.pl $input_bed $genome_selector 1> $out_annotated - 2> $out_log || echo "Error running annotatePeaks." >&2 - - - - - - - - - - - - - - - - - - - - - - - .. class:: infomark - - **Homer annoatePeaks** - More information on accepted formats - http://biowhat.ucsd.edu/homer/ngs/annotation.html - - - - - diff -r 4b5b9c36ff6f -r 4241b517de77 bed2pos.xml --- a/bed2pos.xml Sun Dec 16 23:31:10 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ - - - homer - - - - - bed2pos.pl $input_bed 1> $out_pos - 2> $out_log || echo "Error running bed2pos." >&2 - - - - - - - - - - - - - - - - - - - .. class:: infomark - - **Homer bed2pos.pl** - http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html - - - diff -r 4b5b9c36ff6f -r 4241b517de77 findPeaks.xml --- a/findPeaks.xml Sun Dec 16 23:31:10 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,116 +0,0 @@ - - - homer - - Homer's peakcaller. Requires tag directories (see makeTagDirectory) - - - findPeaks $tagDir.extra_files_path $options -o $outputPeakFile - - #if $control_tagDir: - -i $control_tagDir.extra_files_path - #end if - - 2> $out_log || echo "Error running findPeaks." >&2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - .. class:: infomark - - **Homer findPeaks** - http://biowhat.ucsd.edu/homer/ngs/peaks.html - - Usage: findPeaks <tag directory> [options] - - Finds peaks in the provided tag directory. By default, peak list printed to stdout - - General analysis options: - -o <filename|auto> (file name for to output peaks, default: stdout) - "-o auto" will send output to "<tag directory>/peaks.txt", ".../regions.txt", - or ".../transcripts.txt" depending on the "-style" option - -style <option> (Specialized options for specific analysis strategies) - factor (transcription factor ChIP-Seq, uses -center, output: peaks.txt, default) - histone (histone modification ChIP-Seq, region based, uses -region -size 500 -L 0, regions.txt) - groseq (de novo transcript identification from GroSeq data, transcripts.txt) - tss (TSS identification from 5' RNA sequencing, tss.txt) - dnase (Hypersensitivity [crawford style (nicking)], peaks.txt) - - chipseq/histone options: - -i <input tag directory> (Experiment to use as IgG/Input/Control) - -size <#> (Peak size, default: auto) - -minDist <#> (minimum distance between peaks, default: peak size x2) - -gsize <#> (Set effective mappable genome size, default: 2e9) - -fragLength <#|auto> (Approximate fragment length, default: auto) - -inputFragLength <#|auto> (Approximate fragment length of input tags, default: auto) - -tbp <#> (Maximum tags per bp to count, 0 = no limit, default: auto) - -inputtbp <#> (Maximum tags per bp to count in input, 0 = no limit, default: auto) - -strand <both|separate> (find peaks using tags on both strands or separate, default:both) - -norm # (Tag count to normalize to, default 10000000) - -region (extends start/stop coordinates to cover full region considered "enriched") - -center (Centers peaks on maximum tag overlap and calculates focus ratios) - -nfr (Centers peaks on most likely nucleosome free region [works best with mnase data]) - (-center and -nfr can be performed later with "getPeakTags" - - Peak Filtering options: (set -F/-L/-C to 0 to skip) - -F <#> (fold enrichment over input tag count, default: 4.0) - -P <#> (poisson p-value threshold relative to input tag count, default: 0.0001) - -L <#> (fold enrichment over local tag count, default: 4.0) - -LP <#> (poisson p-value threshold relative to local tag count, default: 0.0001) - -C <#> (fold enrichment limit of expected unique tag positions, default: 2.0) - -localSize <#> (region to check for local tag enrichment, default: 10000) - -inputSize <#> (Size of region to search for control tags, default: 2x peak size) - -fdr <#> (False discovery rate, default = 0.001) - -poisson <#> (Set poisson p-value cutoff, default: uses fdr) - -tagThreshold <#> (Set # of tags to define a peak, default: 25) - -ntagThreshold <#> (Set # of normalized tags to define a peak, by default uses 1e7 for norm) - -minTagThreshold <#> (Absolute minimum tags per peak, default: expected tags per peak) - - GroSeq Options: (Need to specify "-style groseq"): - -tssSize <#> (size of region for initiation detection/artifact size, default: 250) - -minBodySize <#> (size of regoin for transcript body detection, default: 1000) - -maxBodySize <#> (size of regoin for transcript body detection, default: 10000) - -tssFold <#> (fold enrichment for new initiation dectection, default: 4.0) - -bodyFold <#> (fold enrichment for new transcript dectection, default: 4.0) - -endFold <#> (end transcript when levels are this much less than the start, default: 10.0) - -fragLength <#> (Approximate fragment length, default: 150) - -uniqmap <directory> (directory of binary files specifying uniquely mappable locations) - Download from http://biowhat.ucsd.edu/homer/groseq/ - -confPvalue <#> (confidence p-value: 1.00e-05) - -minReadDepth <#> (Minimum initial read depth for transcripts, default: auto) - -pseudoCount <#> (Pseudo tag count, default: 2.0) - -gtf <filename> (Output de novo transcripts in GTF format) - "-o auto" will produce <dir>/transcripts.txt and <dir>/transcripts.gtf - - - - - - diff -r 4b5b9c36ff6f -r 4241b517de77 makeTagDirectory.py --- a/makeTagDirectory.py Sun Dec 16 23:31:10 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,94 +0,0 @@ -""" - - -""" -import re -import os -import sys -import subprocess -import optparse -import shutil -import tempfile - -def getFileString(fpath, outpath): - """ - format a nice file size string - """ - size = '' - fp = os.path.join(outpath, fpath) - s = '? ?' - if os.path.isfile(fp): - n = float(os.path.getsize(fp)) - if n > 2**20: - size = ' (%1.1f MB)' % (n/2**20) - elif n > 2**10: - size = ' (%1.1f KB)' % (n/2**10) - elif n > 0: - size = ' (%d B)' % (int(n)) - s = '%s %s' % (fpath, size) - return s - -class makeTagDirectory(): - """wrapper - """ - - def __init__(self,opts=None, args=None): - self.opts = opts - self.args = args - - def run_makeTagDirectory(self): - """ - makeTagDirectory [options] [alignment file 2] - - """ - if self.opts.format != "bam": - cl = [self.opts.executable] + args + ["-format" , self.opts.format] - else: - cl = [self.opts.executable] + args - print cl - p = subprocess.Popen(cl) - retval = p.wait() - - - html = self.gen_html(args[0]) - #html = self.gen_html() - return html,retval - - def gen_html(self, dr=os.getcwd()): - flist = os.listdir(dr) - print flist - """ add a list of all files in the tagdirectory - """ - res = ['

Files created by makeTagDirectory

\n'] - - flist.sort() - for i,f in enumerate(flist): - if not(os.path.isdir(f)): - fn = os.path.split(f)[-1] - res.append('\n' % (fn,getFileString(fn, dr))) - - res.append('
%s
\n') - - return res - -if __name__ == '__main__': - op = optparse.OptionParser() - op.add_option('-e', '--executable', default='makeTagDirectory') - op.add_option('-o', '--htmloutput', default=None) - op.add_option('-f', '--format', default="sam") - opts, args = op.parse_args() - #assert os.path.isfile(opts.executable),'## makeTagDirectory.py error - cannot find executable %s' % opts.executable - - #if not os.path.exists(opts.outputdir): - #os.makedirs(opts.outputdir) - f = makeTagDirectory(opts, args) - - html,retval = f.run_makeTagDirectory() - f = open(opts.htmloutput, 'w') - f.write(''.join(html)) - f.close() - if retval <> 0: - print >> sys.stderr, serr # indicate failure - - - diff -r 4b5b9c36ff6f -r 4241b517de77 makeTagDirectory.xml --- a/makeTagDirectory.xml Sun Dec 16 23:31:10 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,50 +0,0 @@ - - - homer - - Simple wrapper for makeTagDirectory. Used by findPeaks - - makeTagDirectory.py ${tagDir.files_path} - #for $alignF in $alignmentFiles - $alignF.file -f $alignF.file.ext - #end for - -o $tagDir - 2> $out_log || echo "Error running homer_makeTagDirectory." >&2 - - - - - - - - - - - - - - - - - - - - - - - - - - - .. class:: infomark - - After the job finishes, save the zip file, unzip and open "index.html" - - The actual meme-chip command is displayed under "Command line summary" - - Defaults: - http://meme.nbcr.net/meme/doc/meme-chip.html - - - - diff -r 4b5b9c36ff6f -r 4241b517de77 pos2bed.xml --- a/pos2bed.xml Sun Dec 16 23:31:10 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ - - - homer - - - - - pos2bed.pl $input_peak 1> $out_bed - 2> $out_log || echo "Error running pos2bed." >&2 - - - - - - - - - - - - - - - - - - - .. class:: infomark - - **Homer pos2bed.pl** - http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html - - - diff -r 4b5b9c36ff6f -r 4241b517de77 tool_dependencies.xml --- a/tool_dependencies.xml Sun Dec 16 23:31:10 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ - - - - - - http://biowhat.ucsd.edu/homer/configureHomer.pl - perl ./configureHomer.pl -install - perl ./configureHomer.pl -install hg19 - - $INSTALL_DIR/bin - - - - - Installs homer - - - -