Yes I tried that but it didn't work. The entire output I pasted below in case you are interested. Thanks for your assistance so far, but I think I'm going to give up and just use ubuntu via virtualbox to run galaxy. 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'> 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 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/ctabix.o build/temp.macosx-10.5-i386-2.6/pysam/tabix_util.o build/temp.macosx-10.5-i386-2.6/tabix/bgzf.c.pysam.o build/temp.macosx-10.5-i386-2.6/tabix/bgzip.c.pysam.o build/temp.macosx-10.5-i386-2.6/tabix/index.c.pysam.o build/temp.macosx-10.5-i386-2.6/tabix/knetfile.c.pysam.o build/temp.macosx-10.5-i386-2.6/tabix/kstring.c.pysam.o -lz -o build/lib.macosx-10.5-i386-2.6/ctabix.so 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:
That worked, for everything but pysam. I also tried to install it
Paul Tanger wrote: 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>
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
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",
347, in resolve egg.resolve() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
197, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg line line 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
wrote: 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/