mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
It doesn't make sense to even distribute DRMAA_python eggs. So instead
of downloading its own SGE and linking, scramble now just links to a user-supplied SGE in $SGE_ROOT. Added a seperate script to make it build right on sparc/x86 32/64 Solaris.
This commit is contained in:
Nate Coraor
@@ -1,104 +0,0 @@
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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 +1,81 @@
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import os, sys, shutil
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if "SGE_ROOT" not in os.environ:
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print "scramble(): Please set SGE_ROOT to the path of your SGE installation"
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print "scramble(): before scrambling DRMAA_python"
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sys.exit(1)
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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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# 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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# if our python is 64 bit, use 64 bit sge...
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if sys.maxint < ( 2048 * 1024 * 1024 ):
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if sys.byteorder == 'big':
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arch = "sparc"
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else:
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arch = "x86"
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else:
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if sys.byteorder == 'big':
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arch = "sparc64"
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else:
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arch = "amd64"
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if not "CFLAGS" in os.environ:
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os.environ["CFLAGS"] = ""
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os.environ["CFLAGS"] += " -m64"
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# if we're using sun cc, drop the gcc -Wno-unused option
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import distutils.sysconfig
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cc = distutils.sysconfig.get_config_var('CC')
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if os.popen( cc + ' --version 2>&1' ).read().strip().split('\n')[0].startswith('gcc'):
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compiler = 'gcc'
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elif os.popen( cc + ' -V 2>&1' ).read().strip().split('\n')[0].startswith('cc: Sun C'):
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compiler = 'sun'
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else:
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print "scramble(): Unable to determine compiler"
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sys.exit(1)
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# patch
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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="%s"\n' % os.environ["SGE_ROOT"]
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elif line.startswith('SGE6_ARCH='):
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line = 'SGE6_ARCH="sol-%s"\n' % arch
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elif line.startswith('link_args ='):
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line = 'link_args = [ "-L%s" % os.path.join(SGE6_ROOT, "lib", SGE6_ARCH), "-Wl,-R%s" % os.path.join(SGE6_ROOT, "lib", SGE6_ARCH), "-ldrmaa" ]\n'
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if line == " + [ '-Wno-unused' ]\n":
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if compiler == 'sun':
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line = " #+ [ '-Wno-unused' ]\n"
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print >>o, line,
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i.close()
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o.close()
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# go
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me = sys.argv[0]
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sys.argv = [ me ]
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sys.argv.append( "bdist_egg" )
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execfile( "setup.py", globals(), locals() )
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@@ -1,32 +1,9 @@
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import os, sys, subprocess, tarfile, shutil, urllib2
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import os, sys, shutil
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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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if "SGE_ROOT" not in os.environ:
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print "scramble(): Please set SGE_ROOT to the path of your SGE installation"
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print "scramble(): before scrambling DRMAA_python"
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sys.exit(1)
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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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@@ -44,39 +21,13 @@ except:
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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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# patch
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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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@@ -85,18 +36,15 @@ 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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line = 'SGE6_ROOT="%s"\n' % os.environ["SGE_ROOT"]
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if line.startswith('link_args ='):
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line = 'link_args = [ "-L%s" % os.path.join(SGE6_ROOT, "lib", SGE6_ARCH), "-Wl,-R%s" % os.path.join(SGE6_ROOT, "lib", SGE6_ARCH), "-ldrmaa" ]\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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# go
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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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