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https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
DRMAA build scripts, eggs.ini entry.
And a minor bugfix to eggs.require.
This commit is contained in:
Nate Coraor
@@ -12,6 +12,7 @@ repository = http://eggs.g2.bx.psu.edu
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[eggs:platform]
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bx_python = 0.5.0
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Cheetah = 1.0
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DRMAA_python = 0.2
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MySQL_python = 1.2.2
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pbs_python = 2.9.4
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psycopg2 = 2.0.6
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@@ -54,11 +55,13 @@ python_lzo = _static
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flup = .dev_r2311
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bx_python = _dev_r414
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nose = .dev_r101
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DRMAA_python = _6.1u4
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; source location, necessary for scrambling
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[source]
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bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r414.tar.bz2
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Cheetah = http://umn.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar.gz
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DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz
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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
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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
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psycopg2 = http://initd.org/pub/software/psycopg/PSYCOPG-2-0/psycopg2-2.0.6.tar.gz http://ftp8.us.postgresql.org/postgresql/source/v8.2.6/postgresql-8.2.6.tar.bz2
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@@ -425,10 +425,17 @@ def require( pkg ):
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# there's a conflicting egg on the pythonpath, remove it
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dist = pkg_resources.get_distribution( name )
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working_set = pkg_resources.working_set
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working_set.entries.remove( dist.location )
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# use the canonical path for comparisons
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location = os.path.realpath( dist.location )
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for entry in working_set.entries:
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if os.path.realpath( entry ) == location:
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working_set.entries.remove( entry )
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break
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else:
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raise # some path weirdness has prevented us from finding the offender
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del working_set.by_key[dist.key]
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working_set.entry_keys[dist.location] = []
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sys.path.remove(dist.location)
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working_set.entry_keys[entry] = []
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sys.path.remove(entry)
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# get
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egg.find()
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if not egg.have:
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@@ -0,0 +1,104 @@
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import os, sys, subprocess, tarfile, shutil, urllib2
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def unpack_sge():
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os.makedirs( "gridengine" )
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for file in [ SGE_COMMON_ARCHIVE, SGE_BINARY_PPC_ARCHIVE, SGE_BINARY_X86_ARCHIVE ]:
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if not os.access( file, os.F_OK ):
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fetch( file )
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t = tarfile.open( file, "r" )
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print "unpack_sge() Unpacking:"
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print " ", file
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for fn in t.getnames():
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t.extract( fn, "gridengine" )
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t.close()
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def lipo():
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darwin_dir = os.path.join( "gridengine", "lib", "darwin" )
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os.rename( "%s-ppc" % darwin_dir, "%s-ppc.orig" % darwin_dir )
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os.rename( "%s-x86" % darwin_dir, "%s-x86.orig" % darwin_dir )
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os.makedirs( darwin_dir )
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os.symlink( "darwin", "%s-ppc" % darwin_dir )
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os.symlink( "darwin", "%s-x86" % darwin_dir )
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ppc_libdrmaa = os.path.join( "%s-ppc.orig" % darwin_dir, "libdrmaa.dylib.1.0" )
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x86_libdrmaa = os.path.join( "%s-x86.orig" % darwin_dir, "libdrmaa.dylib.1.0" )
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fat_libdrmaa = os.path.join( darwin_dir, "libdrmaa.dylib.1.0" )
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lipo_cmd = "lipo %s %s -create -output %s" % ( ppc_libdrmaa, x86_libdrmaa, fat_libdrmaa )
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os.symlink( "libdrmaa.dylib.1.0", os.path.join( darwin_dir, "libdrmaa.dylib" ) )
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p = subprocess.Popen( args = lipo_cmd, shell = True )
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r = p.wait()
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if r != 0:
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print "lipo(): lipo failed"
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sys.exit( 1 )
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def fetch( file ):
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url = SGE_BASE_URL + os.path.basename( file )
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print "fetch(): Fetching:"
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print " ", url
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inf = urllib2.urlopen( url )
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otf = open( file, 'wb' )
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otf.write( inf.read() )
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inf.close()
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otf.close()
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# change back to the build dir
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if os.path.dirname( sys.argv[0] ) != "":
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os.chdir( os.path.dirname( sys.argv[0] ) )
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# find setuptools
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scramble_lib = os.path.join( "..", "..", "..", "lib" )
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sys.path.append( scramble_lib )
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try:
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from setuptools import *
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import pkg_resources
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except:
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from ez_setup import use_setuptools
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use_setuptools( download_delay=8, to_dir=scramble_lib )
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from setuptools import *
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import pkg_resources
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# get the tag
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if os.access( ".galaxy_tag", os.F_OK ):
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tagfile = open( ".galaxy_tag", "r" )
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tag = tagfile.readline().strip()
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else:
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tag = None
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SGE_VERSION = ( tag.split( "_" ) )[1]
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SGE_BASE_URL = "http://gridengine.sunsource.net/download/SGE61/"
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SGE_COMMON_ARCHIVE = os.path.abspath( os.path.join( "..", "..", "..", "archives", "ge-%s-common.tar.gz" %SGE_VERSION ) )
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SGE_BINARY_PPC_ARCHIVE = os.path.abspath( os.path.join( "..", "..", "..", "archives", "ge-%s-bin-darwin-ppc.tar.gz" % SGE_VERSION ) )
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SGE_BINARY_X86_ARCHIVE = os.path.abspath( os.path.join( "..", "..", "..", "archives", "ge-%s-bin-darwin-x86.tar.gz" % SGE_VERSION ) )
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# clean, in case you're running this by hand from a dirty module source dir
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for dir in [ "build", "dist", "gridengine" ]:
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if os.access( dir, os.F_OK ):
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print "scramble_it.py: removing dir:", dir
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shutil.rmtree( dir )
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# build/unpack SGE
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unpack_sge()
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lipo()
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file = "setup.py"
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print "scramble(): Patching", file
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if not os.access( "%s.orig" %file, os.F_OK ):
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shutil.copyfile( file, "%s.orig" %file )
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i = open( "%s.orig" %file, "r" )
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o = open( file, "w" )
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for line in i.readlines():
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if line == 'SGE6_ROOT="/scratch_test02/SGE6"\n':
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line = 'SGE6_ROOT="gridengine"\n'
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print >>o, line,
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i.close()
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o.close()
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# tag
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me = sys.argv[0]
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sys.argv = [ me ]
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if tag is not None:
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sys.argv.append( "egg_info" )
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sys.argv.append( "--tag-build=%s" %tag )
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sys.argv.append( "bdist_egg" )
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# go
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execfile( "setup.py", globals(), locals() )
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@@ -0,0 +1,102 @@
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import os, sys, subprocess, tarfile, shutil, urllib2
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def unpack_sge():
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os.makedirs( "gridengine" )
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for file in [ SGE_COMMON_ARCHIVE, SGE_BINARY_ARCHIVE ]:
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if not os.access( file, os.F_OK ):
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fetch( file )
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t = tarfile.open( file, "r" )
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print "unpack_sge() Unpacking:"
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print " ", file
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for fn in t.getnames():
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t.extract( fn, "gridengine" )
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t.close()
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# i doubt you're using a 64 bit python, but if you are, this will break things
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if arch == "sol-x86":
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os.symlink( "sol-x86", os.path.join( "gridengine", "lib", "sol-amd64" ) )
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if arch == "sol-sparc64":
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os.rename( os.path.join( "gridengine", "lib", "sol-sparc64" ), os.path.join( "gridengine", "lib", "sol-sparc64.orig" ) )
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os.symlink( "sol-sparc", os.path.join( "gridengine", "lib", "sol-sparc64" ) )
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def fetch( file ):
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url = SGE_BASE_URL + os.path.basename( file )
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print "fetch(): Fetching:"
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print " ", url
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inf = urllib2.urlopen( url )
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otf = open( file, 'wb' )
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otf.write( inf.read() )
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inf.close()
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otf.close()
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# change back to the build dir
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if os.path.dirname( sys.argv[0] ) != "":
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os.chdir( os.path.dirname( sys.argv[0] ) )
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# find setuptools
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scramble_lib = os.path.join( "..", "..", "..", "lib" )
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sys.path.append( scramble_lib )
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try:
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from setuptools import *
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import pkg_resources
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except:
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from ez_setup import use_setuptools
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use_setuptools( download_delay=8, to_dir=scramble_lib )
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from setuptools import *
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import pkg_resources
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# get the tag
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if os.access( ".galaxy_tag", os.F_OK ):
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tagfile = open( ".galaxy_tag", "r" )
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tag = tagfile.readline().strip()
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else:
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tag = None
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SGE_VERSION = ( tag.split( "_" ) )[1]
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platform = pkg_resources.get_platform()
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if platform.startswith( 'solaris' ):
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if platform.endswith( 'i86pc' ):
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arch = 'sol-x86'
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elif platform.endswith( 'sun4u' ):
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arch = 'sol-sparc64'
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elif platform == 'linux-i686':
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arch = 'lx24-x86'
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elif platform == 'linux-x86_64':
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arch = 'lx24-amd64'
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SGE_BASE_URL = "http://gridengine.sunsource.net/download/SGE61/"
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SGE_COMMON_ARCHIVE = os.path.abspath( os.path.join( "..", "..", "..", "archives", "ge-%s-common.tar.gz" %SGE_VERSION ) )
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SGE_BINARY_ARCHIVE = os.path.abspath( os.path.join( "..", "..", "..", "archives", "ge-%s-bin-%s.tar.gz" %( SGE_VERSION, arch ) ) )
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# clean, in case you're running this by hand from a dirty module source dir
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for dir in [ "build", "dist", "gridengine" ]:
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if os.access( dir, os.F_OK ):
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print "scramble_it.py: removing dir:", dir
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shutil.rmtree( dir )
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# build/unpack SGE
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unpack_sge()
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file = "setup.py"
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print "scramble(): Patching", file
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if not os.access( "%s.orig" %file, os.F_OK ):
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shutil.copyfile( file, "%s.orig" %file )
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i = open( "%s.orig" %file, "r" )
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o = open( file, "w" )
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for line in i.readlines():
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if line == 'SGE6_ROOT="/scratch_test02/SGE6"\n':
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line = 'SGE6_ROOT="gridengine"\n'
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print >>o, line,
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i.close()
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o.close()
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# tag
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me = sys.argv[0]
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sys.argv = [ me ]
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if tag is not None:
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sys.argv.append( "egg_info" )
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sys.argv.append( "--tag-build=%s" %tag )
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sys.argv.append( "bdist_egg" )
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# go
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execfile( "setup.py", globals(), locals() )
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