Mercurial > repos > jjohnson > rsem

changeset 3:59459de65740

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mv RSEM datatypes to separate repository, remove samtools dependency
author Jim Johnson <jj@umn.edu>
date Mon, 10 Mar 2014 07:19:56 -0500
parents 5949673f9e3e
children 30a8343fb0e7
files datatypes_conf.xml repository_dependencies.xml rsem.py rsem_calculate_expression.xml rsem_prepare_reference.xml tool_dependencies.xml
diffstat 6 files changed, 7 insertions(+), 97 deletions(-) [+]
line wrap: on
line diff
--- 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 @@
-<?xml version="1.0"?>
-<datatypes>
-    <datatype_files>
-        <datatype_file name="rsem.py"/>
-    </datatype_files>
-    <registration>
-        <datatype extension="rsem_ref" type="galaxy.datatypes.rsem:RsemReference" display_in_upload="True"/>
-    </registration>
-</datatypes>
-
--- /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 @@
+<?xml version="1.0"?>
+<repositories description="RSEM datatype definitions.">
+    <repository changeset_revision="77151afcd323" name="rsem_datatypes" owner="jjohnson" toolshed="http://toolshed.g2.bx.psu.edu/" />
+</repositories>
--- 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 '<html><head></head><body>AutoGenerated Primary File for RSEM Reference Composite Dataset</body></html>'
-
-    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 = ['<html><head><title>RSEM Reference %s</title></head><p/>Comprises the following files:<p/><ul>' % (refname)]
-        for i,fname in enumerate(flist):
-            sfname = os.path.split(fname)[-1]
-            rval.append( '<li><a href="%s">%s</a>' % ( sfname, sfname ) )
-        rval.append( '</ul></html>' )
-        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/<reference_name>.grp
-        extra_files_path/<reference_name>.ti
-        extra_files_path/<reference_name>.seq
-        extra_files_path/<reference_name>.transcripts.fa
-        Optionally includes files:
-        extra_files_path/<reference_name>.chrlist
-        extra_files_path/<reference_name>.idx.fa
-        extra_files_path/<reference_name>.4.ebwt
-        extra_files_path/<reference_name>.3.ebwt
-        extra_files_path/<reference_name>.2.ebwt
-        extra_files_path/<reference_name>.1.ebwt
-        extra_files_path/<reference_name>.rev.2.ebwt
-        extra_files_path/<reference_name>.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)
-
-
--- 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 @@
   <description>RNA-Seq by Expectation-Maximization</description>
   <requirements>
     <requirement type="package" version="1.1.17">rsem</requirement>
-    <requirement type="package" version="0.1.19">samtools</requirement>
     <requirement type="package" version="1.0.0">bowtie</requirement>
   </requirements>
   <command>
--- 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 @@
     <requirement type="package" version="1.0.0">bowtie</requirement>
   </requirements>
   <command>
+    echo $reference_name " " | tee $reference_file &amp;&amp;
     mkdir $reference_file.extra_files_path &amp;&amp; 
     cd $reference_file.extra_files_path &amp;&amp; 
     rsem-prepare-reference 
@@ -31,6 +32,7 @@
       $reference.reference_fasta_file
     #end if
     $reference_name
+    > ${reference_name}.log
   </command>
   <inputs>
     <conditional name="reference">
@@ -61,7 +63,7 @@
       </help>
     </param>
     <param name="reference_name" type="text" value="rsem_ref_name" label="reference name">
-      <help>A one work name for this RSEM reference containing only letters, digits, and underscore characters</help>
+      <help>A one word name for this RSEM reference containing only letters, digits, and underscore characters</help>
       <validator type="regex" message="Use only letters, digits, and underscore characters">^\w+$</validator>
     </param>
     <conditional name="polya">
--- 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 @@
     <package name="rsem" version="1.1.17">
         <repository changeset_revision="cd7f70d4c687" name="package_rsem_1_1_17" owner="jjohnson" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="samtools" version="0.1.19">
-        <repository changeset_revision="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
     <package name="bowtie" version="1.0.0">
         <repository changeset_revision="9fcaaedbbfd6" name="package_bowtie_1_0_0" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>