Branch merge

lib/galaxy/jobs/runners/__init__.py

@@ -40,7 +40,18 @@ class BaseJobRunner( object ):
         if job_wrapper.dependency_shell_commands:
             commands = "; ".join( job_wrapper.dependency_shell_commands + [ commands ] ) 
 
-        # Append commands to copy job outputs based on from_work_dir attribute.
+        # -- Append commands to copy job outputs based on from_work_dir attribute. --
+
+        # Set up dict of dataset id --> output path; output path can be real or 
+        # false depending on outputs_to_working_directory
+        output_paths = {}
+        for dataset_path in job_wrapper.get_output_fnames():
+            path = dataset_path.real_path
+            if self.app.config.outputs_to_working_directory:
+                path = dataset_path.false_path
+            output_paths[ dataset_path.dataset_id ] = path
+
+        # Walk job's output associations to find and use from_work_dir attributes.
         job = job_wrapper.get_job()
         job_tool = self.app.toolbox.tools_by_id.get( job.tool_id, None )
         for dataset_assoc in job.output_datasets + job.output_library_datasets:
@@ -53,12 +64,13 @@ class BaseJobRunner( object ):
                             # Copy from working dir to HDA.
                             # TODO: move instead of copy to save time?
                             source_file = os.path.join( os.path.abspath( job_wrapper.working_directory ), hda_tool_output.from_work_dir )
+                            destination = output_paths[ dataset.dataset_id ]
                             if in_directory( source_file, job_wrapper.working_directory ):
                                 try:
-                                    commands += "; cp %s %s" % ( source_file, dataset.file_name )
-                                    log.debug( "Copying %s to %s as directed by from_work_dir" % ( source_file, dataset.file_name ) )
+                                    commands += "; cp %s %s" % ( source_file, destination )
+                                    log.debug( "Copying %s to %s as directed by from_work_dir" % ( source_file, destination ) )
                                 except ( IOError, OSError ):
-                                    log.debug( "Could not copy %s to %s as directed by from_work_dir" % ( source_file, dataset.file_name ) )
+                                    log.debug( "Could not copy %s to %s as directed by from_work_dir" % ( source_file, destination ) )
                             else:
                                 # Security violation.
                                 log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) )

lib/galaxy/jobs/runners/lwr.py

@@ -112,16 +112,30 @@ class FileStager(object):
 class Client(object):
     """    
     """
-    def __init__(self, remote_host, job_id):
+    """    
+    """
+    def __init__(self, remote_host, job_id, private_key=None):
         if not remote_host.endswith("/"):
             remote_host = remote_host + "/"
+        ## If we don't have an explicit private_key defined, check for
+        ## one embedded in the URL. A URL of the form
+        ## https://moo@cow:8913 will try to contact https://cow:8913
+        ## with a private key of moo
+        private_key_format = "https?://(.*)@.*/?"
+        private_key_match= re.match(private_key_format, remote_host)
+        if not private_key and private_key_match:
+            private_key = private_key_match.group(1)
+            remote_host = remote_host.replace("%s@" % private_key, '', 1)
         self.remote_host = remote_host
         self.job_id = job_id
+        self.private_key = private_key
 
     def url_open(self, request, data):
         return urllib2.urlopen(request, data)
         
     def __build_url(self, command, args):
+        if self.private_key:
+            args["private_key"] = self.private_key
         data = urllib.urlencode(args)
         url = self.remote_host + command + "?" + data
         return url

lib/galaxy/tools/__init__.py

@@ -1083,7 +1083,9 @@ class Tool:
             help_pages = self.help.findall( "page" )
             help_header = self.help.text
             try:
-                self.help = Template( util.rst_to_html(self.help.text) )
+                self.help = Template( util.rst_to_html(self.help.text), input_encoding='utf-8',
+                                      output_encoding='utf-8', default_filters=[ 'decode.utf8' ],
+                                      encoding_errors='replace' )
             except:
                 log.exception( "error in help for tool %s" % self.name )
             # Multiple help page case
@@ -1093,7 +1095,10 @@ class Tool:
                     help_footer = help_footer + help_page.tail
         # Each page has to rendered all-together because of backreferences allowed by rst
         try:
-            self.help_by_page = [ Template( util.rst_to_html( help_header + x + help_footer ) )
+            self.help_by_page = [ Template( util.rst_to_html( help_header + x + help_footer, 
+                                            input_encoding='utf-8', output_encoding='utf-8', 
+                                            default_filters=[ 'decode.utf8' ],
+                                            encoding_errors='replace' ) )
                                   for x in self.help_by_page ]
         except:
             log.exception( "error in multi-page help for tool %s" % self.name )

tools/rgenetics/rgCaCo.xml

@@ -1,4 +1,5 @@
 <tool id="rgCaCo1" name="Case Control:">
+    <requirements><requirement type="package">plink</requirement></requirements>
     <description>for unrelated subjects</description>
     <command interpreter="python">
         rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$title"  '$out_file1' '$logf' '$logf.files_path' '$gffout'

tools/rgenetics/rgClean.xml

@@ -1,4 +1,5 @@
 <tool id="rgClean1" name="Clean genotypes:">
+    <requirements><requirement type="package">plink</requirement></requirements>
     <description>filter markers, subjects</description>
 
     <command interpreter="python">

tools/rgenetics/rgGLM.xml

@@ -1,4 +1,5 @@
 <tool id="rgGLM1" name="Linear Models:" version="0.2">
+    <requirements><requirement type="package">plink</requirement></requirements>
     <description>for genotype data</description>
     <code file="rgGLM_code.py"/>
     <command interpreter="python">

tools/rgenetics/rgLDIndep.xml

@@ -1,4 +1,5 @@
 <tool id="rgLDIndep1" name="LD Independent:">
+    <requirements><requirement type="package">plink</requirement></requirements>
     <code file="rgLDIndep_code.py"/>
 
     <description>filter high LD pairs - decrease redundancy</description>

tools/rgenetics/rgQC.xml

@@ -1,5 +1,6 @@
 <tool id="rgQC1" name="QC reports:">
-
+    <requirements><requirement type="package">plink</requirement></requirements>
+    
     <description>Marker and Subject measures</description>
 
     <command interpreter="python">

tools/rgenetics/rgTDT.xml

@@ -1,4 +1,6 @@
 <tool id="rgTDT1" name="Transmission Distortion:">
+    <requirements><requirement type="package">plink</requirement></requirements>
+
     <description>for family data</description>
 
     <command interpreter="python">