Mercurial > repos > bgruening > upload_testing
changeset 55:e9cd105a8856
Uploaded
| author | bgruening |
|---|---|
| date | Mon, 12 Aug 2013 09:06:47 -0400 |
| parents | 675d25a0b9d4 |
| children | 07a5042bbe90 |
| files | homer.py tools/makeTagDirectory.xml tools/tool_dependencies.xml |
| diffstat | 3 files changed, 32 insertions(+), 33 deletions(-) [+] |
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--- a/homer.py Mon Aug 12 08:16:21 2013 -0400 +++ b/homer.py Mon Aug 12 09:06:47 2013 -0400 @@ -8,7 +8,7 @@ from galaxy.datatypes.images import Html -class TagDirectory(object): +class TagDirectory( Text ): """Base class for HOMER's Tag Directory datatype.""" file_ext = 'homer_tagdir' @@ -26,6 +26,29 @@ self.add_composite_file('tagGCcontent.txt', description = 'Distribution of fragment GC%-content', mimetype = 'text/html', optional=True) # Distribution of fragment GC%-content. self.add_composite_file('genomeGCcontent.txt', description = 'Distribution of fragment GC%-content at each location in the genome', mimetype = 'text/html', optional=True) # Distribution of fragment GC%-content at each location in the genome. + + def regenerate_primary_file(self,dataset): + """ + cannot do this until we are setting metadata + """ + flist = os.listdir(dataset.extra_files_path) + rval = ['<html><head><title>CuffDiff Output</title></head>'] + rval.append('<body>') + rval.append('<p/>CuffDiff Outputs:<p/><ul>') + for i,fname in enumerate(flist): + sfname = os.path.split(fname)[-1] + rval.append( '<li><a href="%s" type="text/html">%s</a>' % ( sfname, sfname ) ) + rval.append( '</ul></body></html>' ) + f = file(dataset.file_name,'w') + f.write("\n".join( rval )) + f.write('\n') + f.close() + + def set_meta( self, dataset, **kwd ): + Text.set_meta( self, dataset, **kwd ) + self.regenerate_primary_file(dataset) + + def generate_primary_file( self, dataset = None ): rval = ['<html><head><title>HOMER database files</title></head><ul>'] for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems():
--- a/tools/makeTagDirectory.xml Mon Aug 12 08:16:21 2013 -0400 +++ b/tools/makeTagDirectory.xml Mon Aug 12 09:06:47 2013 -0400 @@ -7,17 +7,19 @@ <description>(TagDirectory). Used by findPeaks</description> <!--<version_command></version_command>--> <command> - - export PATH=$PATH:$database.fields.path; + #set $HOMER_PATH = str($database.fields.path) + export PATH=\$PATH:$database.fields.path; - makeTagDirectory $tagdir - #for $infile in alignment_files: - $infile + makeTagDirectory $tag_dir.extra_files_path + #for $infile in $alignment_files: + $infile.file #end for + + 2>&1 </command> <inputs> - <param name="database" type="select" label="HOMER database"> + <param name="database" type="select" label="HOMER database" min="1"> <options from_file="homer.loc"> <column name="value" index="0"/> <column name="name" index="1"/>
--- a/tools/tool_dependencies.xml Mon Aug 12 08:16:21 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="homer" version="4.2"> - <install version="1.0"> - <actions> - <action type="download_file">http://biowhat.ucsd.edu/homer/configureHomer.pl</action> - - <action type="make_directory">$INSTALL_DIR/homer/</action> - <action type="move_file"> - <source>configureHomer.pl</source> - <destination>$INSTALL_DIR/homer/</destination> - </action> - <action type="shell_command">perl .$INSTALL_DIR/homer/configureHomer.pl -install</action> - - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/homer/bin</environment_variable> - </action> - </actions> - </install> - <readme> - I'm sorry but this may not work - - </readme> - </package> -</tool_dependency> -