paul-tangers-macbook-pro:galaxy-dist paultanger$ python scripts/scramble.py -e pysam

pkg_resources is: <module 'pkg_resources' from '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'>

fetch_one(): Using existing source, remove to download again:

/Users/paultanger/galaxy-dist/scripts/scramble/archives/pysam-0.4.2_kanwei_b10f6e722e9a.tar.gz

unpack_source(): Removing old build directory at:

/Users/paultanger/galaxy-dist/scripts/scramble/build/py2.6-macosx-10.5-i386-ucs2/pysam

unpack_source(): Unpacked to:

/Users/paultanger/galaxy-dist/scripts/scramble/build/py2.6-macosx-10.5-i386-ucs2/pysam

copy_build_script(): Using build script /Users/paultanger/galaxy-dist/scripts/scramble/scripts/generic.py

run_scramble_script(): Beginning build

run_scramble_script(): Executing in /Users/paultanger/galaxy-dist/scripts/scramble/build/py2.6-macosx-10.5-i386-ucs2/pysam:

/Library/Frameworks/Python.framework/Versions/6.1/Resources/Python.app/Contents/MacOS/Python scramble.py

pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'>

---------------------------------------------------------------------------

This script requires setuptools version 0.6c11 to run (even to display

help). I will attempt to download it for you (from

http://pypi.python.org/packages/2.6/s/setuptools/), but

you may need to enable firewall access for this script first.

I will start the download in 15 seconds.

(Note: if this machine does not have network access, please obtain the file

http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg

and place it in this directory before rerunning this script.)

---------------------------------------------------------------------------

Downloading http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg

running egg_info

creating pysam.egg-info

writing pysam.egg-info/PKG-INFO

writing top-level names to pysam.egg-info/top_level.txt

writing dependency_links to pysam.egg-info/dependency_links.txt

writing pysam.egg-info/PKG-INFO

writing top-level names to pysam.egg-info/top_level.txt

writing dependency_links to pysam.egg-info/dependency_links.txt

writing manifest file 'pysam.egg-info/SOURCES.txt'

reading manifest file 'pysam.egg-info/SOURCES.txt'

reading manifest template 'MANIFEST.in'

warning: no files found matching 'ez_setup.py'

writing manifest file 'pysam.egg-info/SOURCES.txt'

running bdist_egg

installing library code to build/bdist.macosx-10.5-i386/egg

running install_lib

running build_py

creating build

creating build/lib.macosx-10.5-i386-2.6

creating build/lib.macosx-10.5-i386-2.6/pysam

copying pysam/__init__.py -> build/lib.macosx-10.5-i386-2.6/pysam

copying pysam/Pileup.py -> build/lib.macosx-10.5-i386-2.6/pysam

copying pysam/namedtuple.py -> build/lib.macosx-10.5-i386-2.6/pysam

copying pysam/version.py -> build/lib.macosx-10.5-i386-2.6/pysam

running build_ext

building 'csamtools' extension

creating build/temp.macosx-10.5-i386-2.6

creating build/temp.macosx-10.5-i386-2.6/pysam

creating build/temp.macosx-10.5-i386-2.6/samtools

creating build/temp.macosx-10.5-i386-2.6/samtools/bcftools

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c pysam/csamtools.c -o build/temp.macosx-10.5-i386-2.6/pysam/csamtools.o

pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_7Samfile_9fetch’:

pysam/csamtools.c:8334: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type

pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_7Samfile_10mate’:

pysam/csamtools.c:8725: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type

pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_7Samfile_11count’:

pysam/csamtools.c:9212: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type

pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_7Samfile_12pileup’:

pysam/csamtools.c:9649: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type

pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_16IteratorSNPCalls_2__next__’:

pysam/csamtools.c:26629: warning: this decimal constant is unsigned only in ISO C90

pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_9SNPCaller_1call’:

pysam/csamtools.c:27152: warning: this decimal constant is unsigned only in ISO C90

pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_15IndelCallerBase_2_call’:

pysam/csamtools.c:28600: warning: assignment discards qualifiers from pointer target type

pysam/csamtools.c: In function ‘__Pyx_InitGlobals’:

pysam/csamtools.c:36010: warning: this decimal constant is unsigned only in ISO C90

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c pysam/pysam_util.c -o build/temp.macosx-10.5-i386-2.6/pysam/pysam_util.o

pysam/pysam_util.c: In function ‘pysam_pileup_next’:

pysam/pysam_util.c:190: warning: assignment discards qualifiers from pointer target type

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam2bcf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam2bcf.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam2bcf_indel.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_aux.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_aux.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_color.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_color.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_import.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_import.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_index.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_index.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_lpileup.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_lpileup.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_maqcns.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_maqcns.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_mate.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_mate.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_md.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_md.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_pileup.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_pileup.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_plcmd.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_plcmd.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_rmdup.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_rmdup.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_rmdupse.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_sort.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_sort.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_stat.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_stat.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_tview.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_tview.c.pysam.o

samtools/bam_tview.c.pysam.c:420:2: warning: #warning "No curses library is available; tview is disabled."

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bgzf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bgzf.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/errmod.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/errmod.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/faidx.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/faidx.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/glf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/glf.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/kaln.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/kaln.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/knetfile.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/knetfile.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/kprobaln.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/kprobaln.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/kstring.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/kstring.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/razf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/razf.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/sam.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/sam.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/sam_header.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/sam_header.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/sam_view.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/sam_view.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/sample.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/sample.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/bcf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/bcf.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/bcf2qcall.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/bcf2qcall.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/bcfutils.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/bcfutils.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/call1.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/call1.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/fet.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/fet.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/index.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/index.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/kfunc.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/kfunc.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/ld.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/ld.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/prob1.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/prob1.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/vcf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/vcf.c.pysam.o

gcc -g -L/usr/local/lib -L/Library/Frameworks/Python.framework/Versions/6.1/lib -bundle -undefined dynamic_lookup -arch i386 build/temp.macosx-10.5-i386-2.6/pysam/csamtools.o build/temp.macosx-10.5-i386-2.6/pysam/pysam_util.o build/temp.macosx-10.5-i386-2.6/samtools/bam.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam2bcf.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam2bcf_indel.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_aux.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_color.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_import.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_index.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_lpileup.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_maqcns.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_mate.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_md.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_pileup.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_plcmd.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_rmdup.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_rmdupse.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_sort.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_stat.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_tview.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bgzf.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/errmod.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/faidx.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/glf.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/kaln.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/knetfile.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/kprobaln.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/kstring.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/razf.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/sam.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/sam_header.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/sam_view.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/sample.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/bcf.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/bcf2qcall.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/bcfutils.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/call1.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/fet.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/index.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/kfunc.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/ld.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/prob1.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/vcf.c.pysam.o -lz -o build/lib.macosx-10.5-i386-2.6/csamtools.so

building 'ctabix' extension

creating build/temp.macosx-10.5-i386-2.6/tabix

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c pysam/ctabix.c -o build/temp.macosx-10.5-i386-2.6/pysam/ctabix.o

pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_9Tabixfile_7contigs___get__’:

pysam/ctabix.c:2666: warning: assignment from incompatible pointer type

pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_13TabixIterator_2__next__’:

pysam/ctabix.c:2980: warning: assignment discards qualifiers from pointer target type

pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_2__next__’:

pysam/ctabix.c:7835: warning: assignment discards qualifiers from pointer target type

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c pysam/tabix_util.c -o build/temp.macosx-10.5-i386-2.6/pysam/tabix_util.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c tabix/bgzf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/tabix/bgzf.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c tabix/bgzip.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/tabix/bgzip.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c tabix/index.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/tabix/index.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c tabix/knetfile.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/tabix/knetfile.c.pysam.o

gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c tabix/kstring.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/tabix/kstring.c.pysam.o

creating build/bdist.macosx-10.5-i386

creating build/bdist.macosx-10.5-i386/egg

copying build/lib.macosx-10.5-i386-2.6/csamtools.so -> build/bdist.macosx-10.5-i386/egg

copying build/lib.macosx-10.5-i386-2.6/ctabix.so -> build/bdist.macosx-10.5-i386/egg

creating build/bdist.macosx-10.5-i386/egg/pysam

copying build/lib.macosx-10.5-i386-2.6/pysam/__init__.py -> build/bdist.macosx-10.5-i386/egg/pysam

copying build/lib.macosx-10.5-i386-2.6/pysam/namedtuple.py -> build/bdist.macosx-10.5-i386/egg/pysam

copying build/lib.macosx-10.5-i386-2.6/pysam/Pileup.py -> build/bdist.macosx-10.5-i386/egg/pysam

copying build/lib.macosx-10.5-i386-2.6/pysam/version.py -> build/bdist.macosx-10.5-i386/egg/pysam

byte-compiling build/bdist.macosx-10.5-i386/egg/pysam/__init__.py to __init__.pyc

byte-compiling build/bdist.macosx-10.5-i386/egg/pysam/namedtuple.py to namedtuple.pyc

byte-compiling build/bdist.macosx-10.5-i386/egg/pysam/Pileup.py to Pileup.pyc

byte-compiling build/bdist.macosx-10.5-i386/egg/pysam/version.py to version.pyc

creating stub loader for csamtools.so

creating stub loader for ctabix.so

byte-compiling build/bdist.macosx-10.5-i386/egg/csamtools.py to csamtools.pyc

byte-compiling build/bdist.macosx-10.5-i386/egg/ctabix.py to ctabix.pyc

creating build/bdist.macosx-10.5-i386/egg/EGG-INFO

copying pysam.egg-info/PKG-INFO -> build/bdist.macosx-10.5-i386/egg/EGG-INFO

copying pysam.egg-info/SOURCES.txt -> build/bdist.macosx-10.5-i386/egg/EGG-INFO

copying pysam.egg-info/dependency_links.txt -> build/bdist.macosx-10.5-i386/egg/EGG-INFO

copying pysam.egg-info/not-zip-safe -> build/bdist.macosx-10.5-i386/egg/EGG-INFO

copying pysam.egg-info/top_level.txt -> build/bdist.macosx-10.5-i386/egg/EGG-INFO

writing build/bdist.macosx-10.5-i386/egg/EGG-INFO/native_libs.txt

creating dist

creating 'dist/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-macosx-10.5-i386.egg' and adding 'build/bdist.macosx-10.5-i386/egg' to it

removing 'build/bdist.macosx-10.5-i386/egg' (and everything under it)

Traceback (most recent call last):

File "scripts/scramble.py", line 50, in <module>

egg.scramble()

File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/scramble.py", line 60, in scramble

raise ScrambleFailure( self, "%s(): Egg build for %s did not appear to fail, but no egg found to copy from expected path:\n %s" % ( sys._getframe().f_code.co_name, self.name, new_egg ) )

galaxy.eggs.scramble.ScrambleFailure: scramble(): Egg build for pysam did not appear to fail, but no egg found to copy from expected path:

/Users/paultanger/galaxy-dist/scripts/scramble/build/py2.6-macosx-10.5-i386-ucs2/pysam/dist/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-macosx-10.5-i386-ucs2.egg

paul-tangers-macbook-pro:galaxy-dist paultanger$

On Mon, Aug 29, 2011 at 12:37 PM, Nate Coraor <nate@bx.psu.edu> wrote:

Paul Tanger wrote:
> I don't know if I did this correctly, but the output from
> python get_platforms.py
> is:
> macosx-10.5-i386-ucs2

Okay, it looks like EPD python is only compiled for one platform. To
use this, you'll need to scramble your own versions of the eggs which
use C code. Could you try scrambling pysam as instructed below and see
what the results are? You will have to do this for each egg that can't
be downloaded.

--nate

>
> On Mon, Aug 29, 2011 at 12:13 PM, Nate Coraor <nate@bx.psu.edu> wrote:
>
> > Paul Tanger wrote:
> > > That worked, for everything but pysam. I also tried to install it
> > directly:
> > >
> > > pysam 0.4.2 couldn't be downloaded automatically. You can try
> > > building it by hand with:
> > > python scripts/scramble.py -e pysam
> > >
> > > Some eggs are out of date, attempting to fetch...
> > >
> > > pkg_resources is: <module 'pkg_resources' from
> > > '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'>
> > > pysam 0.4.2 couldn't be downloaded automatically. You can try
> > > building it by hand with:
> > > python scripts/scramble.py -e pysam
> > > Fetch failed.
> >
> > What platform do you get from:
> >
> > python ./scripts/get_platforms.py
> >
> > ? Note that this needs to have the path changed from append to insert
> > as in the previous scripts.
> >
> > Thanks,
> > --nate
> >
> > >
> > > On Mon, Aug 29, 2011 at 10:51 AM, Nate Coraor <nate@bx.psu.edu> wrote:
> > >
> > > > Paul Tanger wrote:
> > > > > Getting somewhere, but it looks like it can't find numpy 1.6?
> > > > > error returned is:
> > > > >
> > > > > pkg_resources is: <module 'pkg_resources' from
> > > > > '/Users/paultanger/galaxy-dist/lib/pkg_resources.py'>
> > > > > Some eggs are out of date, attempting to fetch...
> > > > >
> > > > > pkg_resources is: <module 'pkg_resources' from
> > > > > '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'>
> > > > > Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
> > > > > Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg
> > > > > Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg
> > > > > Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg
> > > > > Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg
> > > > > Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg
> > > > > Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg
> > > > > Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg
> > > > > Fetched
> > > > http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg
> > > > > Fetched
> > http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg
> > > > > Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg
> > > > > Traceback (most recent call last):
> > > > > File "./scripts/fetch_eggs.py", line 32, in <module>
> > > > > c.resolve() # Only fetch eggs required by the config
> > > > > File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> > line
> > > > > 347, in resolve
> > > > > egg.resolve()
> > > > > File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> > line
> > > > > 197, in resolve
> > > > > return self.version_conflict( e.args[0], e.args[1] )
> > > > > File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> > line
> > > > > 228, in version_conflict
> > > > > r = pkg_resources.working_set.resolve( ( dist.as_requirement(),
> > ),
> > > > env,
> > > > > egg.fetch )
> > > > > File "/Users/paultanger/galaxy-dist/lib/pkg_resources.py", line
> > 565, in
> > > > > resolve
> > > > > raise DistributionNotFound(req) # XXX put more info here
> > > > > pkg_resources.DistributionNotFound: numpy==1.6.0
> > > > > Fetch failed.
> > > >
> > > > It could be a conflict with the existing version, try:
> > > >
> > > > python -ES ./scripts/fetch_eggs.py
> > > >
> > > > --nate
> > > >
> > > > >
> > > > > On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor <nate@bx.psu.edu>
> > wrote:
> > > > >
> > > > > > Paul Tanger wrote:
> > > > > > > sys path is:
> > > > > > >
> > > > > > > ['/Users/paultanger/galaxy-dist/scripts',
> > > > > > > '/Users/paultanger/python/scripts',
> > > > > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip',
> > > > > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6',
> > > > > > >
> > > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin',
> > > > > > >
> > > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac',
> > > > > > >
> > > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages',
> > > > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk',
> > > > > > >
> > > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old',
> > > > > > >
> > > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload',
> > > > > > >
> > > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages',
> > > > > > >
> > > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL',
> > > > > > > '/Users/paultanger/galaxy-dist/lib']
> > > > > >
> > > > > > Hi Paul,
> > > > > >
> > > > > > If you replace:
> > > > > >
> > > > > > lib = os.path.abspath( os.path.join( os.path.dirname( __file__
> > ),
> > > > "..",
> > > > > > "lib" ) )
> > > > > > sys.path.append( lib )
> > > > > >
> > > > > > With:
> > > > > >
> > > > > > lib = os.path.abspath( os.path.join( os.path.dirname( __file__
> > ),
> > > > "..",
> > > > > > "lib" ) )
> > > > > > sys.path.insert( 0, lib )
> > > > > >
> > > > > > In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have
> > an
> > > > > > effect?
> > > > > >
> > > > > > --nate
> > > > > >
> > > > > > >
> > > > > > > pkg_resources is:
> > > > > > > <module 'pkg_resources' from
> > > > > > >
> > > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'>
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger <
> > > > paul.tanger@colostate.edu
> > > > > > >wrote:
> > > > > > >
> > > > > > > > It is free for academic use. I'll try what you suggested below
> > -
> > > > > > thanks!
> > > > > > > >
> > > > > > > >
> > > > > > > > On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor <nate@bx.psu.edu>
> > > > wrote:
> > > > > > > >
> > > > > > > >> Paul Tanger wrote:
> > > > > > > >> > Yes it works with the default python install. Any way I can
> > get
> > > > it
> > > > > > > >> working
> > > > > > > >> > with EPD python?
> > > > > > > >>
> > > > > > > >> I've never worked with EPD and since it's not free it's
> > unlikely
> > > > we
> > > > > > can
> > > > > > > >> do much debugging on it here. It would appear that they
> > bundle a
> > > > > > > >> version of pkg_resources which changes the
> > DistributionNotFound
> > > > class,
> > > > > > > >> but it's hard to know exactly what's going on here.
> > > > > > > >>
> > > > > > > >> One thing that might shed a bit of light on it would be to
> > print
> > > > > > > >> sys.path and pkg_resources at the top of:
> > > > > > > >>
> > > > > > > >> galaxy-dist/lib/galaxy/eggs/__init__.py
> > > > > > > >>
> > > > > > > >> After the import of pkg_resources and see which version it's
> > > > using.
> > > > > > > >>
> > > > > > > >> --nate
> > > > > > > >>
> > > > > > > >> >
> > > > > > > >> > On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor <
> > nate@bx.psu.edu>
> > > > > > wrote:
> > > > > > > >> >
> > > > > > > >> > > Paul Tanger wrote:
> > > > > > > >> > > > Has anyone gotten galaxy installed on a mac 10.5 with
> > EPD
> > > > > > > >> (enthought)
> > > > > > > >> > > python
> > > > > > > >> > > > 2.6 (EPD version 6.1-1)? I get this error which I
> > suspect
> > > > is
> > > > > > > >> related to
> > > > > > > >> > > the
> > > > > > > >> > > > fact that I have EPD python, not the generic python that
> > was
> > > > > > > >> > > preinstalled?
> > > > > > > >> > > > Any ideas?
> > > > > > > >> > > >
> > > > > > > >> > > > Thanks!
> > > > > > > >> > > >
> > > > > > > >> > > > Some eggs are out of date, attempting to fetch...
> > > > > > > >> > > > Traceback (most recent call last):
> > > > > > > >> > > > File "./scripts/fetch_eggs.py", line 30, in <module>
> > > > > > > >> > > > c.resolve() # Only fetch eggs required by the config
> > > > > > > >> > > > File
> > > > > > "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> > > > > > > >> line
> > > > > > > >> > > > 345, in resolve
> > > > > > > >> > > > egg.resolve()
> > > > > > > >> > > > File
> > > > > > "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> > > > > > > >> line
> > > > > > > >> > > > 184, in resolve
> > > > > > > >> > > > if e.args[0].project_name !=
> > > > self.distribution.project_name:
> > > > > > > >> > > > AttributeError: 'str' object has no attribute
> > 'project_name'
> > > > > > > >> > > > Fetch failed.
> > > > > > > >> > >
> > > > > > > >> > > Hi Paul,
> > > > > > > >> > >
> > > > > > > >> > > Can you give it a try with the system Python and see if
> > you
> > > > get
> > > > > > the
> > > > > > > >> same
> > > > > > > >> > > result? All you need to do is put:
> > > > > > > >> > >
> > > > > > > >> > >
> > > > /System/Library/Frameworks/Python.framework/Versions/2.6/bin
> > > > > > > >> > >
> > > > > > > >> > > At the head of your $PATH.
> > > > > > > >> > >
> > > > > > > >> > > Thanks,
> > > > > > > >> > > --nate
> > > > > > > >> > >
> > > > > > > >> > > >
> > ___________________________________________________________
> > > > > > > >> > > > Please keep all replies on the list by using "reply all"
> > > > > > > >> > > > in your mail client. To manage your subscriptions to
> > this
> > > > > > > >> > > > and other Galaxy lists, please use the interface at:
> > > > > > > >> > > >
> > > > > > > >> > > > http://lists.bx.psu.edu/
> > > > > > > >> > >
> > > > > > > >> > >
> > > > > > > >>
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > _____________________________________
> > > > > Paul Tanger
> > > > > NSF IGERT Bioenergy Fellow
> > > > >
> > > > > Bioagricultural Sciences and Pest Management
> > > > > Colorado State University
> > > > > 1177 Campus Delivery
> > > > > Fort Collins, CO 80523-1177
> > > > >
> > > > > paul.tanger@colostate.edu
> > > > > http://bioenergy-igert.colostate.edu/
> > > >
> > >
> > >
> > >
> > > --
> > > _____________________________________
> > > Paul Tanger
> > > NSF IGERT Bioenergy Fellow
> > >
> > > Bioagricultural Sciences and Pest Management
> > > Colorado State University
> > > 1177 Campus Delivery
> > > Fort Collins, CO 80523-1177
> > >
> > > paul.tanger@colostate.edu
> > > http://bioenergy-igert.colostate.edu/
> >
>
>
>
> --
> _____________________________________
> Paul Tanger
> NSF IGERT Bioenergy Fellow
>
> Bioagricultural Sciences and Pest Management
> Colorado State University
> 1177 Campus Delivery
> Fort Collins, CO 80523-1177
>
> paul.tanger@colostate.edu
> http://bioenergy-igert.colostate.edu/

--
_____________________________________
Paul Tanger
NSF IGERT Bioenergy Fellow

Bioagricultural Sciences and Pest Management
Colorado State University
1177 Campus Delivery
Fort Collins, CO 80523-1177

paul.tanger@colostate.edu
http://bioenergy-igert.colostate.edu/