# HG changeset patch # User kevyin # Date 1355721920 18000 # Node ID 83dffd6d773397091303cf95a3dce1ae91dc3107 # Parent 7efeace8bd32d0383d260de4aae1cb04dea4e3eb Deleted selected files diff -r 7efeace8bd32 -r 83dffd6d7733 README --- a/README Mon Dec 17 00:22:39 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 7efeace8bd32 -r 83dffd6d7733 annotatePeaks.xml --- a/annotatePeaks.xml Mon Dec 17 00:22:39 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,55 +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 and options - - http://biowhat.ucsd.edu/homer/ngs/annotation.html - - TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format. - - - - diff -r 7efeace8bd32 -r 83dffd6d7733 bed2pos.xml --- a/bed2pos.xml Mon Dec 17 00:22:39 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ - - - homer - - - - - bed2pos.pl $input_bed 1> $out_pos - 2> $out_log || echo "Error running bed2pos." >&2 - - - - - - - - - - - - - - - - - - - .. class:: infomark - - Converts: BED -(to)-> homer peak positions - - **Homer bed2pos.pl** - - http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html - - - diff -r 7efeace8bd32 -r 83dffd6d7733 findPeaks.xml --- a/findPeaks.xml Mon Dec 17 00:22:39 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,58 +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** - - For more options, look under: "Command line options for findPeaks" - - http://biowhat.ucsd.edu/homer/ngs/peaks.html - - TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format. - - - - diff -r 7efeace8bd32 -r 83dffd6d7733 makeTagDirectory.py --- a/makeTagDirectory.py Mon Dec 17 00:22:39 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 7efeace8bd32 -r 83dffd6d7733 makeTagDirectory.xml --- a/makeTagDirectory.xml Mon Dec 17 00:22:39 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +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 - - **Homer makeTagDirectory** - - For more options, look under: "Command line options" - - http://biowhat.ucsd.edu/homer/ngs/tagDir.html - - - - - diff -r 7efeace8bd32 -r 83dffd6d7733 pos2bed.xml --- a/pos2bed.xml Mon Dec 17 00:22:39 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ - - - homer - - - - - pos2bed.pl $input_peak 1> $out_bed - 2> $out_log || echo "Error running pos2bed." >&2 - - - - - - - - - - - - - - - - - - - .. class:: infomark - - Converts: homer peak positions -(to)-> BED format - - **Homer pos2bed.pl** - - http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html - - - diff -r 7efeace8bd32 -r 83dffd6d7733 tool_dependencies.xml --- a/tool_dependencies.xml Mon Dec 17 00:22:39 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 - - - -