Separate framework and tool environments.

Whether running locally or via PBS, $PATH should now be handled in your user's environment. This also fixes problems like PYTHONPATH on the new blast nodes being wrong (because they are x86_64 and the frontends are i686). Note that you can actually start Galaxy without having an eggs dir now.
galaxyproject · Apr 11, 2008 · 7560751 · 7560751
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diff --git a/eggs.ini b/eggs.ini
@@ -1,46 +1,48 @@
 ;
-; Galaxy egg version, download and build configuration.
+; Galaxy egg version configuration
+;
+; This file is version controlled and should not be edited by hand!
+; For more information, see:
+;   http://g2.trac.bx.psu.edu/wiki/GalaxyEggs
 ;
 
 [general]
 repository = http://eggs.g2.bx.psu.edu
 
-; <python_module> = <version> <download_url>
-[eggs]
-; platform specific
-bx_python = 0.5.0 http://dist.g2.bx.psu.edu/bx-python_dist-r414.tar.bz2
-Cheetah = 1.0 http://umn.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar.gz
-MySQL_python = 1.2.2 http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python-1.2.2.tar.gz
-pbs_python = 2.9.4 http://ftp.sara.nl/pub/outgoing/pbs_python-2.9.4.tar.gz
-psycopg2 = 2.0.6 http://initd.org/pub/software/psycopg/psycopg2-2.0.6.tar.gz
-pycrypto = 2.0.1 http://www.amk.ca/files/python/crypto/pycrypto-2.0.1.tar.gz
-pysqlite = 2.3.5 http://initd.org/pub/software/pysqlite/releases/2.3/2.3.5/pysqlite-2.3.5.tar.gz
-python_lzo = 1.08 http://www.oberhumer.com/opensource/lzo/download/LZO-v1/python-lzo-1.08.tar.gz
-threadframe = 0.2 http://www.majid.info/python/threadframe/threadframe-0.2.tar.gz
-; platform inspecific
-Beaker = 0.5 http://cheeseshop.python.org/packages/source/B/Beaker/Beaker-0.5.tar.gz
-docutils = 0.4 http://downloads.sourceforge.net/docutils/docutils-0.4.tar.gz
-elementtree = 1.2.6_20050316 http://effbot.org/downloads/elementtree-1.2.6-20050316.tar.gz
-flup = 0.5 http://www.saddi.com/software/flup/dist/flup-r2311.tar.gz
-lrucache = 0.2 http://evan.prodromou.name/lrucache/lrucache-0.2.tar.gz
+[eggs:platform]
+bx_python = 0.5.0
+Cheetah = 1.0
+MySQL_python = 1.2.2
+pbs_python = 2.9.4
+psycopg2 = 2.0.6
+pycrypto = 2.0.1
+pysqlite = 2.3.5
+python_lzo = 1.08
+threadframe = 0.2
+
+[eggs:noplatform]
+Beaker = 0.5
+docutils = 0.4
+elementtree = 1.2.6_20050316
+flup = 0.5
+lrucache = 0.2
 ;lsprof - james
-Mako = 0.1.10 http://www.makotemplates.org/downloads/Mako-0.1.10.tar.gz
-MyghtyUtils = 0.52 http://cheeseshop.python.org/packages/source/M/MyghtyUtils/MyghtyUtils-0.52.zip
-nose = 0.9.1 http://www.somethingaboutorange.com/mrl/projects/nose/nose-0.9.1.tar.gz
-NoseHTML = 0.2 http://dist.g2.bx.psu.edu/nosehtml_dist-0.2.tar.bz2
-Paste = 1.5.1 http://cheeseshop.python.org/packages/source/P/Paste/Paste-1.5.1.tar.gz
-PasteDeploy = 1.3.1 http://cheeseshop.python.org/packages/source/P/PasteDeploy/PasteDeploy-1.3.1.tar.gz
-PasteScript = 1.3.6 http://cheeseshop.python.org/packages/source/P/PasteScript/PasteScript-1.3.6.tar.gz
-Routes = 1.6.3 http://pypi.python.org/packages/source/R/Routes/Routes-1.6.3.tar.gz
-simplejson = 1.5 http://cheeseshop.python.org/packages/source/s/simplejson/simplejson-1.5.tar.gz
-SQLAlchemy = 0.3.11 http://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.3.11.tar.gz
-Tempita = 0.1 http://pypi.python.org/packages/source/T/Tempita/Tempita-0.1.tar.gz
-twill = 0.8.3 http://darcs.idyll.org/~t/projects/twill-0.8.3.tar.gz
-;twill = 0.9 http://darcs.idyll.org/~t/projects/twill-0.9.tar.gz
-WebError = 0.8a http://pypi.python.org/packages/source/W/WebError/WebError-0.8a.tar.gz
-WebHelpers = 0.2 http://pypi.python.org/packages/source/W/WebHelpers/WebHelpers-0.2.tar.gz
-WebOb = 0.8.5 http://pypi.python.org/packages/source/W/WebOb/WebOb-0.8.5.tar.gz
-wsgiref = 0.1.2 http://pypi.python.org/packages/source/w/wsgiref/wsgiref-0.1.2.zip
+Mako = 0.1.10
+MyghtyUtils = 0.52
+nose = 0.9.1
+NoseHTML = 0.2
+Paste = 1.5.1
+PasteDeploy = 1.3.1
+PasteScript = 1.3.6
+Routes = 1.6.3
+simplejson = 1.5
+SQLAlchemy = 0.3.11
+Tempita = 0.1
+twill = 0.8.3
+WebError = 0.8a
+WebHelpers = 0.2
+WebOb = 0.8.5
+wsgiref = 0.1.2
 
 ; extra version information
 [tags]
@@ -53,46 +55,35 @@ flup = .dev_r2311
 bx_python = _dev_r414
 nose = .dev_r101
 
-; When using scramble.py, you may force scramble to build eggs for one of the
-; following platforms by providing the platform as the second command line
-; argument.  Scramble will then ssh to the host defined and use the python
-; interpreter defined to build the egg.  This is mainly intended for Galaxy
-; developers at Penn State who maintain the pre-built egg repository.  To build
-; eggs for your own platform, just leave off the platform argument to
-; scramble.py.
-[hosts]
-py2.4-linux-i686-ucs2 = scofield.bx.psu.edu /depot/projects/pythons/linux-i686-ucs2/bin/python2.4
-py2.4-linux-i686-ucs4 = scofield.bx.psu.edu /depot/projects/pythons/linux-i686-ucs4/bin/python2.4
-py2.5-linux-i686-ucs2 = scofield.bx.psu.edu /depot/projects/pythons/linux-i686-ucs2/bin/python2.5
-py2.5-linux-i686-ucs4 = scofield.bx.psu.edu /depot/projects/pythons/linux-i686-ucs4/bin/python2.5
-py2.4-linux-x86_64-ucs2 = herbie.bx.psu.edu /depot/projects/pythons/linux-x86_64-ucs2/bin/python2.4
-py2.4-linux-x86_64-ucs4 = herbie.bx.psu.edu /depot/projects/pythons/linux-x86_64-ucs4/bin/python2.4
-py2.5-linux-x86_64-ucs2 = herbie.bx.psu.edu /depot/projects/pythons/linux-x86_64-ucs2/bin/python2.5
-py2.5-linux-x86_64-ucs4 = herbie.bx.psu.edu /depot/projects/pythons/linux-x86_64-ucs4/bin/python2.5
-py2.4-macosx-10.3-fat-ucs2 = medeski.bx.psu.edu /usr/local/bin/python2.4
-py2.5-macosx-10.3-fat-ucs2 = medeski.bx.psu.edu /usr/local/bin/python2.5
-py2.4-solaris-2.11-i86pc-ucs2 = victory.bx.psu.edu /depot/projects/pythons/solaris-2.11-i86pc-ucs2/bin/python2.4
-py2.5-solaris-2.11-i86pc-ucs2 = victory.bx.psu.edu /depot/projects/pythons/solaris-2.11-i86pc-ucs2/bin/python2.5
-py2.4-solaris-2.10-sun4u-ucs2 = v880.bx.psu.edu /depot/projects/pythons/solaris-2.10-sun4u-ucs2/bin/python2.4
-py2.5-solaris-2.10-sun4u-ucs2 = v880.bx.psu.edu /depot/projects/pythons/solaris-2.10-sun4u-ucs2/bin/python2.5
-
-; Instead of providing a platform name as the third argument, you may also
-; provide one of these platform group names.  Platforms on the right side of the
-; assignment in [groups] must exist on the left side of an assignment in the
-; [hosts] section.  Penn State Galaxy developers building eggs for distribution
-; should use 'all' for platform-specific eggs and 'all-noplatform' for
-; platform-inspecific eggs.
-[groups]
-py2.4-linux = py2.4-linux-i686-ucs2 py2.4-linux-i686-ucs4 py2.4-linux-x86_64-ucs2 py2.4-linux-x86_64-ucs4
-py2.5-linux = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4
-linux = py2.4-linux-i686-ucs2 py2.4-linux-i686-ucs4 py2.4-linux-x86_64-ucs2 py2.4-linux-x86_64-ucs4 py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4
-py2.4-macosx = py2.4-macosx-10.3-fat-ucs2
-py2.5-macosx = py2.5-macosx-10.3-fat-ucs2
-macosx = py2.4-macosx-10.3-fat-ucs2 py2.5-macosx-10.3-fat-ucs2
-py2.4-solaris = py2.4-solaris-2.11-i86pc-ucs2 py2.4-solaris-2.10-sun4u-ucs2
-py2.5-solaris = py2.5-solaris-2.11-i86pc-ucs2 py2.5-solaris-2.10-sun4u-ucs2
-solaris = py2.4-solaris-2.11-i86pc-ucs2 py2.4-solaris-2.10-sun4u-ucs2 py2.5-solaris-2.11-i86pc-ucs2 py2.5-solaris-2.10-sun4u-ucs2
-py2.4-all = py2.4-linux-i686-ucs2 py2.4-linux-i686-ucs4 py2.4-linux-x86_64-ucs2 py2.4-linux-x86_64-ucs4 py2.4-macosx-10.3-fat-ucs2 py2.4-solaris-2.11-i86pc-ucs2 py2.4-solaris-2.10-sun4u-ucs2
-py2.5-all = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 py2.5-macosx-10.3-fat-ucs2 py2.5-solaris-2.11-i86pc-ucs2 py2.5-solaris-2.10-sun4u-ucs2
-all = py2.4-linux-i686-ucs2 py2.4-linux-i686-ucs4 py2.4-linux-x86_64-ucs2 py2.4-linux-x86_64-ucs4 py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 py2.4-macosx-10.3-fat-ucs2 py2.5-macosx-10.3-fat-ucs2 py2.4-solaris-2.11-i86pc-ucs2 py2.4-solaris-2.10-sun4u-ucs2 py2.5-solaris-2.11-i86pc-ucs2 py2.5-solaris-2.10-sun4u-ucs2
-all-noplatform = py2.4-solaris-2.11-i86pc-ucs2 py2.5-solaris-2.11-i86pc-ucs2
+; source location, necessary for scrambling
+[source]
+bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r414.tar.bz2
+Cheetah = http://umn.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar.gz
+MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python-1.2.2.tar.gz http://mysql.mirrors.pair.com/Downloads/MySQL-5.0/mysql-5.0.51a.tar.gz
+pbs_python = http://ftp.sara.nl/pub/outgoing/pbs_python-2.9.4.tar.gz http://www.clusterresources.com/downloads/torque/torque-%s.tar.gz
+psycopg2 = http://initd.org/pub/software/psycopg/psycopg2-2.0.6.tar.gz http://ftp8.us.postgresql.org/postgresql/source/v8.2.6/postgresql-8.2.6.tar.bz2
+pycrypto = http://www.amk.ca/files/python/crypto/pycrypto-2.0.1.tar.gz
+pysqlite = http://initd.org/pub/software/pysqlite/releases/2.3/2.3.5/pysqlite-2.3.5.tar.gz http://www.sqlite.org/sqlite-source-3_5_4.zip
+python_lzo = http://www.oberhumer.com/opensource/lzo/download/LZO-v1/python-lzo-1.08.tar.gz http://www.oberhumer.com/opensource/lzo/download/LZO-v1/lzo-1.08.tar.gz
+threadframe = http://www.majid.info/python/threadframe/threadframe-0.2.tar.gz
+Beaker = http://cheeseshop.python.org/packages/source/B/Beaker/Beaker-0.5.tar.gz
+docutils = http://downloads.sourceforge.net/docutils/docutils-0.4.tar.gz
+elementtree = http://effbot.org/downloads/elementtree-1.2.6-20050316.tar.gz
+flup = http://www.saddi.com/software/flup/dist/flup-r2311.tar.gz
+lrucache = http://evan.prodromou.name/lrucache/lrucache-0.2.tar.gz
+Mako = http://www.makotemplates.org/downloads/Mako-0.1.10.tar.gz
+MyghtyUtils = http://cheeseshop.python.org/packages/source/M/MyghtyUtils/MyghtyUtils-0.52.zip
+nose = http://www.somethingaboutorange.com/mrl/projects/nose/nose-0.9.1.tar.gz
+NoseHTML = http://dist.g2.bx.psu.edu/nosehtml-0.2.tar.bz2
+Paste = http://cheeseshop.python.org/packages/source/P/Paste/Paste-1.5.1.tar.gz
+PasteDeploy = http://cheeseshop.python.org/packages/source/P/PasteDeploy/PasteDeploy-1.3.1.tar.gz
+PasteScript = http://cheeseshop.python.org/packages/source/P/PasteScript/PasteScript-1.3.6.tar.gz
+Routes = http://pypi.python.org/packages/source/R/Routes/Routes-1.6.3.tar.gz
+simplejson = http://cheeseshop.python.org/packages/source/s/simplejson/simplejson-1.5.tar.gz
+SQLAlchemy = http://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.3.11.tar.gz
+Tempita = http://pypi.python.org/packages/source/T/Tempita/Tempita-0.1.tar.gz
+twill = http://darcs.idyll.org/~t/projects/twill-0.8.3.tar.gz
+WebError = http://pypi.python.org/packages/source/W/WebError/WebError-0.8a.tar.gz
+WebHelpers = http://pypi.python.org/packages/source/W/WebHelpers/WebHelpers-0.2.tar.gz
+WebOb = http://pypi.python.org/packages/source/W/WebOb/WebOb-0.8.5.tar.gz
+wsgiref = http://pypi.python.org/packages/source/w/wsgiref/wsgiref-0.1.2.zip
diff --git a/lib/galaxy/eggs/__init__.py b/lib/galaxy/eggs/__init__.py
@@ -3,6 +3,7 @@
 """
 
 import os, sys, shutil, tarfile, zipfile, subprocess, ConfigParser, glob, urllib2
+from types import ModuleType
 
 import logging
 log = logging.getLogger( __name__ )
@@ -13,6 +14,9 @@
 # within tools.  i don't know of any way around this. -ndc
 galaxy_dir = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "..", ".." ) )
 
+class NewEgg( Exception ):
+    pass
+
 class EggNotFetchable( Exception ):
     pass
 
@@ -406,6 +410,8 @@ def require( pkg ):
         else:
             pkg_resources.working_set.require( "%s==%s" % ( name, egg.get_vertag() ) )
         return
+    except UserWarning, e:
+        sys.exit( 1 )
     except pkg_resources.VersionConflict, e:
         # there's a conflicting egg on the pythonpath, remove it
         dist = pkg_resources.get_distribution( name )
@@ -419,9 +425,17 @@ def require( pkg ):
         if not egg.have:
             if not egg.fetch():
                 raise EggNotFetchable( egg.name )
+            pkg_resources.working_set.require( "%s==%s" % ( name, egg.get_vertag() ) )
+            if dist.project_name in sys.modules:
+                try:
+                    mod = sys.modules[dist.project_name]
+                    reload( mod )
+                except:
+                    raise NewEgg( "Galaxy downloaded a new egg (%s) but was unable to reload the module it contained.  Please try starting Galaxy again." % egg.name )
     except pkg_resources.DistributionNotFound, e:
 	# the initial require itself is the first dep, but it can have
 	# multiple deps, which will be fetched by the require below.
+        print >>sys.stdout, "foo"
         dep = pkg_resources.Requirement.parse( str( e ) ).project_name
         egg = c.get_for_require( dep )
         if egg is None:
@@ -431,7 +445,8 @@ def require( pkg ):
         if not egg.have:
             if not egg.fetch():
                 raise EggNotFetchable( egg.name )
-    require( pkg )
+            pkg_resources.working_set.require( "%s==%s" % ( name, egg.get_vertag() ) )
+    #require( pkg )
 
 # convenience stuff
 def get_ucs():

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
@@ -264,6 +264,7 @@ def __init__(self, job_id, tool, queue ):
         self.extra_filenames = []
         self.working_directory = None
         self.command_line = None
+        self.galaxy_lib_dir = None
 
     def get_param_dict( self ):
         """
@@ -318,6 +319,9 @@ def prepare( self ):
         param_filename = self.tool.build_param_file( param_dict, self.working_directory )
         # Build the job's command line
         self.command_line = self.tool.build_command_line( param_dict )
+        # FIXME: for now, tools get Galaxy's lib dir in their path
+        if self.command_line.startswith( 'python' ):
+            self.galaxy_lib_dir = os.path.abspath( "lib" ) # cwd = galaxy root
         # command_line won't actually be set in the db until finish unless you do it here
         # We need it in the db to be able to restart jobs -ndc
         job.command_line = self.command_line

diff --git a/lib/galaxy/jobs/runners/local.py b/lib/galaxy/jobs/runners/local.py
@@ -53,13 +53,21 @@ def run_job( self, job_wrapper ):
             return
         # If we were able to get a command line, run the job
         if command_line:
+            if job_wrapper.galaxy_lib_dir is not None:
+                if 'PYTHONPATH' in os.environ:
+                    env = { 'PYTHONPATH' : "%s:%s" % ( os.environ['PYTHONPATH'], job_wrapper.galaxy_lib_dir ) } 
+                else:
+                    env = { 'PYTHONPATH' : job_wrapper.galaxy_lib_dir }
+            else:
+                env = {}
             try:
                 log.debug( 'executing: %s' % command_line )
                 proc = subprocess.Popen( args = command_line, 
                                          shell = True, 
                                          cwd = job_wrapper.working_directory, 
                                          stdout = subprocess.PIPE, 
                                          stderr = subprocess.PIPE,
+                                         env = env,
                                          preexec_fn = os.setpgrp )
                 job_wrapper.set_runner( 'local:///', proc.pid )
                 stdout = proc.stdout.read() 

diff --git a/lib/galaxy/jobs/runners/pbs.py b/lib/galaxy/jobs/runners/pbs.py
@@ -6,6 +6,7 @@
 from Queue import Queue, Empty
 
 from galaxy import model
+from paste.deploy.converters import asbool
 
 import pkg_resources
 
@@ -18,17 +19,27 @@
 log = logging.getLogger( __name__ )
 
 pbs_template = """#!/bin/sh
-export LC_ALL='%s'
-export PATH='%s'
-export PYTHONPATH='%s'
+GALAXY_LIB="%s"
+if [ "$GALAXY_LIB" != "None" ]; then
+    if [ -n "$PYTHONPATH" ]; then
+        export PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
+    else
+        export PYTHONPATH="$GALAXY_LIB"
+    fi
+fi
 cd %s
 %s
 """
 
 pbs_symlink_template = """#!/bin/sh
-export LC_ALL='%s'
-export PATH='%s'
-export PYTHONPATH='%s'
+GALAXY_LIB="%s"
+if [ "$GALAXY_LIB" != "None" ]; then
+    if [ -n "$PYTHONPATH" ]; then
+        export PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
+    else
+        export PYTHONPATH="$GALAXY_LIB"
+    fi
+fi
 for dataset in %s; do
     dir=`dirname $dataset`
     file=`basename $dataset`
@@ -168,9 +179,9 @@ def queue_job( self, job_wrapper ):
 
         # write the job script
         if self.app.config.pbs_stage_path != '':
-            script = pbs_symlink_template % (os.environ['LC_ALL'], os.environ['NODEPATH'], os.environ['PYTHONPATH'], " ".join(job_wrapper.get_input_fnames() + job_wrapper.get_output_fnames()), self.app.config.pbs_stage_path, exec_dir, command_line)
+            script = pbs_symlink_template % (job_wrapper.galaxy_lib_dir, " ".join(job_wrapper.get_input_fnames() + job_wrapper.get_output_fnames()), self.app.config.pbs_stage_path, exec_dir, command_line)
         else:
-            script = pbs_template % (os.environ['LC_ALL'], os.environ['NODEPATH'], os.environ['PYTHONPATH'], exec_dir, command_line)
+            script = pbs_template % (job_wrapper.galaxy_lib_dir, exec_dir, command_line)
         job_file = "%s/database/pbs/%s.sh" % (os.getcwd(), job_wrapper.job_id)
         fh = file(job_file, "w")
         fh.write(script)
@@ -347,12 +358,13 @@ def finish_job( self, pbs_job_state ):
             log.exception("Job wrapper finish method failed")
 
         # clean up the job_file, ofile, efile
-        if os.access(ofile, os.R_OK):
-            os.unlink(ofile)
-        if os.access(efile, os.R_OK):
-            os.unlink(efile)
-        if os.access(job_file, os.R_OK):
-            os.unlink(job_file)
+        if not asbool( self.app.config.get( 'debug', False ) ):
+            if os.access(ofile, os.R_OK):
+                os.unlink(ofile)
+            if os.access(efile, os.R_OK):
+                os.unlink(efile)
+            if os.access(job_file, os.R_OK):
+                os.unlink(job_file)
 
     def put( self, job_wrapper ):
         """Add a job to the queue (by job identifier)"""

diff --git a/nosetests.sh b/nosetests.sh
diff --git a/run.sh b/run.sh
@@ -1,18 +1,4 @@
 #!/bin/sh
 
-. ./scripts/get_python.sh
-. ./setup_paths.sh
-
-# Create directories
-CREATE_DIRS="
-$UNIVERSE_HOME/database/$CREATE_DIR/files
-$UNIVERSE_HOME/database/$CREATE_DIR/tmp
-"
-
-for CREATE_DIR in $CREATE_DIRS; do
-    if [ ! -d $CREATE_DIR -o ! -h $CREATE_DIR ]; then
-        mkdir -p $CREATE_DIR
-    fi
-done
-
-$GALAXY_PYTHON ./scripts/paster.py serve universe_wsgi.ini $@
+cd `dirname $0`
+python -ES ./scripts/paster.py serve universe_wsgi.ini $@
diff --git a/run_functional_tests.sh b/run_functional_tests.sh
@@ -5,24 +5,24 @@
 rm -f run_functional_tests.log 
 
 if [ ! $1 ]; then
-	./nosetests.sh -v -w test --with-nosehtml --html-report-file run_functional_tests.html --exclude="^get" functional
+	python -ES ./scripts/nosetests.py -v -w test --with-nosehtml --html-report-file run_functional_tests.html --exclude="^get" functional
 elif [ $1 = 'help' ]; then
 	echo "'run_functional_tests.sh'                       for testing all the tools in functional directory"
 	echo "'run_functional_tests.sh aaa'                   for testing one test case of 'aaa' ('aaa' is the file name with path)"
 	echo "'run_functional_tests.sh -id bbb'               for testing one tool with id 'bbb' ('bbb' is the tool id)"
 	echo "'run_functional_tests.sh -sid ccc'              for testing one section with sid 'ccc' ('ccc' is the string after 'section::')"
 	echo "'run_functional_tests.sh -list'                 for listing all the tool ids"
 elif [ $1 = '-id' ]; then
-	./nosetests.sh -v -w test functional.test_toolbox:TestForTool_$2 --with-nosehtml --html-report-file run_functional_tests.html
+	python -ES ./scripts/nosetests.py -v -w test functional.test_toolbox:TestForTool_$2 --with-nosehtml --html-report-file run_functional_tests.html
 elif [ $1 = '-sid' ]; then
-        ./nosetests.sh --with-nosehtml --html-report-file run_functional_tests.html -v -w test `python tool_list.py $2`
+        python -ES ./scripts/nosetests.py --with-nosehtml --html-report-file run_functional_tests.html -v -w test `python tool_list.py $2`
 elif [ $1 = '-list' ]; then
         python tool_list.py
 	echo "==========================================================================================================================================="
 	echo "'run_functional_tests.sh -id bbb'               for testing one tool with id 'bbb' ('bbb' is the tool id)"
 	echo "'run_functional_tests.sh -sid ccc'              for testing one section with sid 'ccc' ('ccc' is the string after 'section::')"
 else
-	./nosetests.sh -v -w test --with-nosehtml --html-report-file run_functional_tests.html $1
+	python -ES ./scripts/nosetests.py -v -w test --with-nosehtml --html-report-file run_functional_tests.html $1
 fi
 
 echo "'run_functional_tests.sh help'                  for help"