Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.

scripts/cleanup_datasets.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/env python
 
 import sys, os, time, ConfigParser
 from datetime import datetime, timedelta
@@ -9,6 +9,8 @@ import pkg_resources
 pkg_resources.require( "sqlalchemy>=0.3" )
 from sqlalchemy import eagerload
 
+assert sys.version_info[:2] >= ( 2, 4 )
+
 def main():
     parser = OptionParser()
     parser.add_option( "-d", "--days", dest="days", action="store", type="int", help="number of days (60)", default=60 )

scripts/get_platforms.py

@@ -1,4 +1,8 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/env python
+
+import sys
+
+assert sys.version_info[:2] >= ( 2, 4 )
 
 from eggs import get_full_platform, get_noplatform
 print get_noplatform()

scripts/microbes/README.txt

@@ -6,19 +6,19 @@ Step 3 requires a binary 'faToNib' to properly generate sequence files.
 Steps should be performed in the order they appear here.
 
 (1.) To Download and process Genome Projects from NCBI into a form usable by Galaxy:
-	python2.4 /GALAXY_ROOT/scripts/microbes/harvest_bacteria.py /OUTPUT/DIRECTORY/microbes/ > /OUTPUT/DIRECTORY/harvest.txt
+	python /GALAXY_ROOT/scripts/microbes/harvest_bacteria.py /OUTPUT/DIRECTORY/microbes/ > /OUTPUT/DIRECTORY/harvest.txt
 
 (2.) To Walk downloaded Genome Projects and Convert, in place, IDs to match the UCSC Archaea browser, where applicable:
-	python2.4 /GALAXY_ROOT/scripts/microbes/ncbi_to_ucsc.py /OUTPUT/DIRECTORY/microbes/ > /OUTPUT/DIRECTORY/ncbi_to_ucsc.txt
+	python /GALAXY_ROOT/scripts/microbes/ncbi_to_ucsc.py /OUTPUT/DIRECTORY/microbes/ > /OUTPUT/DIRECTORY/ncbi_to_ucsc.txt
 
 (3.) To create nib files (for extraction) and to generate the location file content for Microbes used for extracting Genomic DNA:
-	python2.4 /GALAXY_ROOT/scripts/microbes/create_nib_seq_loc_file.py /OUTPUT/DIRECTORY/microbes/ seq.loc > /OUTPUT/DIRECTORY/sequence.txt
+	python /GALAXY_ROOT/scripts/microbes/create_nib_seq_loc_file.py /OUTPUT/DIRECTORY/microbes/ seq.loc > /OUTPUT/DIRECTORY/sequence.txt
 
 (4.) To create the location file for the Microbial Data Resource tool in Galaxy:
-	python2.4 /GALAXY_ROOT/scripts/microbes/create_bacteria_loc_file.py /OUTPUT/DIRECTORY/microbes/ > /OUTPUT/DIRECTORY/microbial_data.loc
+	python /GALAXY_ROOT/scripts/microbes/create_bacteria_loc_file.py /OUTPUT/DIRECTORY/microbes/ > /OUTPUT/DIRECTORY/microbial_data.loc
 
 (5.) To Generate a single file containing the lengths for each chromosome for each species, to be added to 'manual_builds.txt':
-	python2.4 /GALAXY_ROOT/scripts/microbes/get_builds_lengths.py /OUTPUT/DIRECTORY/microbes/ > /OUTPUT/DIRECTORY/microbes.len
+	python /GALAXY_ROOT/scripts/microbes/get_builds_lengths.py /OUTPUT/DIRECTORY/microbes/ > /OUTPUT/DIRECTORY/microbes.len
 
 (6.) To Create the Wiki Table listing available Microbial Data in Galaxy:
-	python2.4 /GALAXY_ROOT/scripts/microbes/create_bacteria_table.py /OUTPUT/DIRECTORY/microbes/ > /OUTPUT/DIRECTORY/microbes.table
+	python /GALAXY_ROOT/scripts/microbes/create_bacteria_table.py /OUTPUT/DIRECTORY/microbes/ > /OUTPUT/DIRECTORY/microbes.table

scripts/microbes/create_bacteria_loc_file.py

@@ -1,8 +1,10 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/env python
 #Dan Blankenberg
 
 import sys, os
 
+assert sys.version_info[:2] >= ( 2, 4 )
+
 def __main__():
     base_dir = os.path.join( os.getcwd(), "bacteria" )
     try:

scripts/microbes/create_bacteria_table.py

@@ -1,8 +1,10 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/env python
 #Dan Blankenberg
 
 import sys, os
 
+assert sys.version_info[:2] >= ( 2, 4 )
+
 def __main__():
     base_dir = os.path.join( os.getcwd(), "bacteria" )
     try:

scripts/microbes/create_nib_seq_loc_file.py

@@ -1,8 +1,10 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/env python
 #Dan Blankenberg
 
 import sys, os
 
+assert sys.version_info[:2] >= ( 2, 4 )
+
 def __main__():
     base_dir = os.path.join( os.getcwd(), "bacteria" )
     try:

scripts/microbes/get_builds_lengths.py

@@ -1,8 +1,10 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/env python
 #Dan Blankenberg
 
 import sys, os
 
+assert sys.version_info[:2] >= ( 2, 4 )
+
 def __main__():
     base_dir = os.path.join( os.getcwd(), "bacteria" )
     try:

scripts/microbes/harvest_bacteria.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/env python
 #Dan Blankenberg
 
 #Harvest Bacteria
@@ -12,6 +12,8 @@ from ftplib import FTP
 from BeautifulSoup import BeautifulSoup
 from util import get_bed_from_genbank, get_bed_from_glimmer3, get_bed_from_GeneMarkHMM, get_bed_from_GeneMark
 
+assert sys.version_info[:2] >= ( 2, 4 )
+
 #this defines the types of ftp files we are interested in, and how to process/convert them to a form for our use
 desired_ftp_files = {'GeneMark':{'ext':'GeneMark-2.5f','parser':'process_GeneMark'},
                     'GeneMarkHMM':{'ext':'GeneMarkHMM-2.6m','parser':'process_GeneMarkHMM'},

scripts/microbes/util.py

@@ -1,8 +1,10 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/env python
 #Dan Blankenberg
 
 import sys
 
+assert sys.version_info[:2] >= ( 2, 4 )
+
 #genbank_to_bed
 class Region:
     def __init__( self ):

scripts/nosetests.py

@@ -1,9 +1,11 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/env python
 # EASY-INSTALL-ENTRY-SCRIPT: 'nose','console_scripts','nosetests'
 __requires__ = 'nose'
 import sys
 from pkg_resources import load_entry_point
 
+assert sys.version_info[:2] >= ( 2, 4 )
+
 sys.exit(
    load_entry_point('nose', 'console_scripts', 'nosetests')()
 )

scripts/paster.py

@@ -1,4 +1,8 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/env python
+
+import sys
+
+assert sys.version_info[:2] >= ( 2, 4 )
 
 import pkg_resources; 
 pkg_resources.require( "PasteScript" )

scripts/remove_renamed_datasets_from_disk.py

@@ -1,11 +1,13 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/env python
 """
 Removes a dataset file ( which was first renamed by appending _purged to the file name ) from disk.
-Usage: python2.4 remove_renamed_datasets_from_disk.py renamed.log
+Usage: python remove_renamed_datasets_from_disk.py renamed.log
 """
 
 import sys, os
 
+assert sys.version_info[:2] >= ( 2, 4 )
+
 def main():
     infile = sys.argv[1]
     outfile = infile + ".removed.log"

scripts/rename_purged_datasets.py

@@ -1,11 +1,13 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/env python
 """
 Renames a dataset file by appending _purged to the file name so that it can later be removed from disk.
-Usage: python2.4 rename_purged_datasets.py purge.log
+Usage: python rename_purged_datasets.py purge.log
 """
 
 import sys, os
 
+assert sys.version_info[:2] >= ( 2, 4 )
+
 def main():
     infile = sys.argv[1]
     outfile = infile + ".renamed.log"

scripts/update_dataset_size.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/env python
 """
 Updates dataset.size column.
 Remember to backup your database before running.
@@ -7,6 +7,7 @@ Remember to backup your database before running.
 import sys, os, ConfigParser
 import galaxy.app
 
+assert sys.version_info[:2] >= ( 2, 4 )
 
 def main():
     ini_file = sys.argv.pop(1)

scripts/update_metadata.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/env python
 #Dan Blankenberg
 """
 Updates metadata in the database to match rev 1891.
@@ -11,6 +11,7 @@ import galaxy.app
 from galaxy.util.bunch import Bunch
 import galaxy.datatypes.tabular
 
+assert sys.version_info[:2] >= ( 2, 4 )
 
 def main():
     ini_file = sys.argv.pop(1)