# HG changeset patch # User Jim Johnson # Date 1394453996 18000 # Node ID 59459de657404279aa611b2edf5e7ec67c594a6c # Parent 5949673f9e3e83c6c171010bb02f54558e13557c mv RSEM datatypes to separate repository, remove samtools dependency diff -r 5949673f9e3e -r 59459de65740 datatypes_conf.xml --- a/datatypes_conf.xml Fri Feb 07 07:34:29 2014 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ - - - - - - - - - - diff -r 5949673f9e3e -r 59459de65740 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Mon Mar 10 07:19:56 2014 -0500 @@ -0,0 +1,4 @@ + + + + diff -r 5949673f9e3e -r 59459de65740 rsem.py --- a/rsem.py Fri Feb 07 07:34:29 2014 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ -""" -RSEM datatypes -""" -import os,os.path,re,sys -import galaxy.datatypes.data -from galaxy.datatypes.images import Html -from galaxy.datatypes.metadata import MetadataElement - -class RsemReference( Html ): - """Class describing an RSEM reference""" - MetadataElement( name='reference_name', default=None, desc='RSEM Reference Name', readonly=True, visible=True, no_value=None ) - - file_ext = 'rsem_ref' - is_binary = True - composite_type = 'auto_primary_file' - allow_datatype_change = False - - def generate_primary_file( self, dataset = None ): - """ - This is called only at upload to write the html file - cannot rename the datasets here - they come with the default unfortunately - """ - return 'AutoGenerated Primary File for RSEM Reference Composite Dataset' - - def regenerate_primary_file(self,dataset): - """ - cannot do this until we are setting metadata - """ - refname = dataset.metadata.reference_name - flist = os.listdir(dataset.extra_files_path) - rval = ['RSEM Reference %s

Comprises the following files:

' ) - f = file(dataset.file_name,'w') - f.write("\n".join( rval )) - f.write('\n') - f.close() - - def set_peek( self, dataset, is_multi_byte=False ): - if not dataset.dataset.purged: - dataset.peek = "RSEM Reference (%s)" % ( dataset.metadata.reference_name ) - dataset.blurb = "RSEM Reference (%s)" % ( dataset.metadata.reference_name ) - else: - dataset.peek = 'RSEM Reference (%s) does not exist' % ( dataset.metadata.reference_name ) - dataset.blurb = 'RSEM Reference (%s) purged from disk' % ( dataset.metadata.reference_name ) - - def display_peek( self, dataset ): - try: - return dataset.peek - except: - return "RSEM Reference" - - def set_meta( self, dataset, overwrite = True, **kwd ): - """ - Expecting files: - extra_files_path/.grp - extra_files_path/.ti - extra_files_path/.seq - extra_files_path/.transcripts.fa - Optionally includes files: - extra_files_path/.chrlist - extra_files_path/.idx.fa - extra_files_path/.4.ebwt - extra_files_path/.3.ebwt - extra_files_path/.2.ebwt - extra_files_path/.1.ebwt - extra_files_path/.rev.2.ebwt - extra_files_path/.rev.1.ebwt - """ - pat = '^(.*)\.grp$' - efp = dataset.extra_files_path - flist = os.listdir(efp) - for i,fname in enumerate(flist): - m = re.match(pat,fname) - if m: - dataset.metadata.reference_name = m.groups()[0] - break - self.regenerate_primary_file(dataset) - - diff -r 5949673f9e3e -r 59459de65740 rsem_calculate_expression.xml --- a/rsem_calculate_expression.xml Fri Feb 07 07:34:29 2014 -0600 +++ b/rsem_calculate_expression.xml Mon Mar 10 07:19:56 2014 -0500 @@ -2,7 +2,6 @@ RNA-Seq by Expectation-Maximization rsem - samtools bowtie diff -r 5949673f9e3e -r 59459de65740 rsem_prepare_reference.xml --- a/rsem_prepare_reference.xml Fri Feb 07 07:34:29 2014 -0600 +++ b/rsem_prepare_reference.xml Mon Mar 10 07:19:56 2014 -0500 @@ -5,6 +5,7 @@ bowtie + echo $reference_name " " | tee $reference_file && mkdir $reference_file.extra_files_path && cd $reference_file.extra_files_path && rsem-prepare-reference @@ -31,6 +32,7 @@ $reference.reference_fasta_file #end if $reference_name + > ${reference_name}.log @@ -61,7 +63,7 @@ - A one work name for this RSEM reference containing only letters, digits, and underscore characters + A one word name for this RSEM reference containing only letters, digits, and underscore characters ^\w+$ diff -r 5949673f9e3e -r 59459de65740 tool_dependencies.xml --- a/tool_dependencies.xml Fri Feb 07 07:34:29 2014 -0600 +++ b/tool_dependencies.xml Mon Mar 10 07:19:56 2014 -0500 @@ -3,9 +3,6 @@ - - -