July 2013 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Strange issue with Data Libraries
by Patel, Viren 12 Jul '13

12 Jul '13

To follow-up on my original query, after turning on full web server logging, one strange thing I see in the web server access log is that the actual request is a bit different from the link URL. Here is the link URL: https://<galaxy-fqdn>/galaxy/library_admin/browse_libraries?sort=name&f-description=All&f-name=All&f-deleted=False&operation=browse&id=7e3ef68f693c8dd0<https://galaxy.emory.edu/galaxy/library_admin/browse_libraries?sort=name&f-…> And here is the get request that shows up in the web server log: GET /galaxy/library_admin/browse_libraries?async=false&sort=name&page=1&show_item_checkboxes=false&operation=browse&id=7e3ef68f693c8dd0&f-deleted=False&f-name=All&f-description=All HTTP/1.1 - HTTP/1.1 302 Found The 302 is a temporary redirect, but why? I don't think I am doing any redirects in the web server, other than http to https and I even disabled this to no effect. The other question in my mind is why the logged URL is different from the actual link URL. Is this a web server thing? If so I will crawl back into my hole…. ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

1 0

Cloudman - Software does not work due to broken symlinks
by Ravpreet Setia 12 Jul '13

12 Jul '13

This may be a problem with the latest Galaxy Cloudman AMI. Some tools (tophat is one) are failing to run because they cannot be found. I have noticed that after launching a new instance with the latest AMI, the "<package>/<version>/default" sym-links under /mnt/galaxy/tools point to a directory in /mnt/galaxyTools, which does not exist since this new AMI merged galaxyTools and galaxyData. Additionally, even after manually fixing the symlink and the path in the env.sh file (it also references galaxyTools), running tophat would fail, although now, at least, it can find the program. This may be an issue with tophat's XML or python script though, since I fixed Velvet's symlink and env.sh and it worked perfectly. This document explains how the default symlink and env.sh are used by Galaxy: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies Thanks for any suggestions.

2 2

pbs_python Scramble Continues to Fail
by Frost Mitchell 12 Jul '13

12 Jul '13

Hi. We are attempting to set up a Galaxy instance on our local TORQUE cluster, but the Documentation instructions to scramble as such: LIBTORQUE_DIR=/path/to/libtorque python scripts/scramble.py -e pbs_python Gives the following barrage of output: (galaxy_env)[root@galaxy galaxy-dist]# LIBTORQUE_DIR=/rc/tools/free/redhat_6_x86_64/torque-4.2.2/lib/ python scripts/scramble.py -e pbs_python --config=universe_wsgi.ini fetch_one(): Using existing source, remove to download again: /rc/galaxy/galaxy-dist/scripts/scramble/archives/pbs_python-4.1.0.tar.gz unpack_source(): Removing old build directory at: /rc/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs4/pbs_python unpack_source(): Unpacked to: /rc/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs4/pbs_python copy_build_script(): Using build script /rc/galaxy/galaxy-dist/scripts/scramble/scripts/pbs_python.py run_scramble_script(): Beginning build run_scramble_script(): Executing in /rc/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs4/pbs_python: /rc/galaxy/tools/galaxy_env/bin/python scramble.py checking for pbs-config... /rc/tools/free/redhat_6_x86_64/torque-4.2.2/lib//../bin/pbs-config Found torque version: 4.2.2 checking for python... /rc/galaxy/tools/galaxy_env/bin/python checking for python version... 2.6 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.6/site-packages checking for python extension module directory... ${exec_prefix}/lib64/python2.6/site-packages configure: creating ./config.status config.status: creating Makefile config.status: creating setup.py scramble(): Patching setup.py running egg_info creating src/pbs_python.egg-info writing src/pbs_python.egg-info/PKG-INFO writing top-level names to src/pbs_python.egg-info/top_level.txt writing dependency_links to src/pbs_python.egg-info/dependency_links.txt writing manifest file 'src/pbs_python.egg-info/SOURCES.txt' reading manifest file 'src/pbs_python.egg-info/SOURCES.txt' writing manifest file 'src/pbs_python.egg-info/SOURCES.txt' running bdist_egg installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib.linux-x86_64-2.6 copying src/pbs.py -> build/lib.linux-x86_64-2.6 copying src/PBSQuery.py -> build/lib.linux-x86_64-2.6 running build_ext building '_pbs' extension creating build/temp.linux-x86_64-2.6 creating build/temp.linux-x86_64-2.6/src gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DTORQUE_OLD -I/usr/include/python2.6 -c src/pbs_wrap.c -o build/temp.linux-x86_64-2.6/src/pbs_wrap.o src/pbs_wrap.c:124:20: error: Python.h: No such file or directory src/pbs_wrap.c:730: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:785: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:806: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c: In function ‘SWIG_Python_AddErrorMsg’: src/pbs_wrap.c:853: error: ‘PyObject’ undeclared (first use in this function) src/pbs_wrap.c:853: error: (Each undeclared identifier is reported only once src/pbs_wrap.c:853: error: for each function it appears in.) src/pbs_wrap.c:853: error: ‘type’ undeclared (first use in this function) src/pbs_wrap.c:854: error: ‘value’ undeclared (first use in this function) src/pbs_wrap.c:855: error: ‘traceback’ undeclared (first use in this function) src/pbs_wrap.c:857: warning: implicit declaration of function ‘PyErr_Occurred’ src/pbs_wrap.c:857: warning: implicit declaration of function ‘PyErr_Fetch’ src/pbs_wrap.c:859: error: ‘old_str’ undeclared (first use in this function) src/pbs_wrap.c:859: warning: implicit declaration of function ‘PyObject_Str’ src/pbs_wrap.c:860: warning: implicit declaration of function ‘PyErr_Clear’ src/pbs_wrap.c:861: warning: implicit declaration of function ‘Py_XINCREF’ src/pbs_wrap.c:862: warning: implicit declaration of function ‘PyErr_Format’ src/pbs_wrap.c:862: warning: implicit declaration of function ‘PyString_AsString’ src/pbs_wrap.c:863: warning: implicit declaration of function ‘Py_DECREF’ src/pbs_wrap.c:866: warning: implicit declaration of function ‘PyErr_SetString’ src/pbs_wrap.c:866: error: ‘PyExc_RuntimeError’ undeclared (first use in this function) src/pbs_wrap.c: At top level: src/pbs_wrap.c:1034: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1042: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1053: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1060: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1106: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1208: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1219: error: expected specifier-qualifier-list before ‘PyObject’ src/pbs_wrap.c: In function ‘SWIG_Python_CheckImplicit’: src/pbs_wrap.c:1231: error: ‘PySwigClientData’ has no member named ‘implicitconv’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:1234: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1243: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c: In function ‘PySwigClientData_Del’: src/pbs_wrap.c:1298: warning: implicit declaration of function ‘Py_XDECREF’ src/pbs_wrap.c:1298: error: ‘PySwigClientData’ has no member named ‘newraw’ src/pbs_wrap.c:1299: error: ‘PySwigClientData’ has no member named ‘newargs’ src/pbs_wrap.c:1300: error: ‘PySwigClientData’ has no member named ‘destroy’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:1306: error: expected specifier-qualifier-list before ‘PyObject_HEAD’ src/pbs_wrap.c:1313: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1319: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1337: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1343: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1349: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1372: error: expected declaration specifiers or ‘...’ before ‘FILE’ src/pbs_wrap.c: In function ‘PySwigObject_print’: src/pbs_wrap.c:1377: error: ‘PyObject’ undeclared (first use in this function) src/pbs_wrap.c:1377: error: ‘repr’ undeclared (first use in this function) src/pbs_wrap.c:1377: warning: implicit declaration of function ‘PySwigObject_repr’ src/pbs_wrap.c:1380: warning: implicit declaration of function ‘fputs’ src/pbs_wrap.c:1380: error: ‘fp’ undeclared (first use in this function) src/pbs_wrap.c: At top level: src/pbs_wrap.c:1388: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c: In function ‘PySwigObject_compare’: src/pbs_wrap.c:1399: error: ‘PySwigObject’ has no member named ‘ptr’ src/pbs_wrap.c:1400: error: ‘PySwigObject’ has no member named ‘ptr’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:1404: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1406: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1413: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1418: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1422: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1456: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1473: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1489: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1501: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1513: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1561: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘swigobject_methods’ src/pbs_wrap.c:1573: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1580: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1688: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1706: error: expected specifier-qualifier-list before ‘PyObject_HEAD’ src/pbs_wrap.c:1713: error: expected declaration specifiers or ‘...’ before ‘FILE’ src/pbs_wrap.c: In function ‘PySwigPacked_print’: src/pbs_wrap.c:1716: error: ‘fp’ undeclared (first use in this function) src/pbs_wrap.c:1717: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1717: error: ‘PySwigPacked’ has no member named ‘size’ src/pbs_wrap.c:1721: error: ‘PySwigPacked’ has no member named ‘ty’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:1726: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1737: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c: In function ‘PySwigPacked_compare’: src/pbs_wrap.c:1751: error: ‘PySwigPacked’ has no member named ‘size’ src/pbs_wrap.c:1752: error: ‘PySwigPacked’ has no member named ‘size’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘size’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘size’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘size’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: warning: left-hand operand of comma expression has no effect src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: warning: left-hand operand of comma expression has no effect src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: warning: left-hand operand of comma expression has no effect src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: warning: left-hand operand of comma expression has no effect src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘size’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:1757: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1759: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1766: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1772: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1781: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1851: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1871: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1887: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1893: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1903: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1954: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1969: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2060: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2092: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2114: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:2178: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2199: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:2217: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:2238: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c: In function ‘SWIG_Python_GetModule’: src/pbs_wrap.c:2259: warning: implicit declaration of function ‘PyCObject_Import’ src/pbs_wrap.c:2260: warning: assignment makes pointer from integer without a cast src/pbs_wrap.c: At top level: src/pbs_wrap.c:2274: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c: In function ‘SWIG_Python_DestroyModule’: src/pbs_wrap.c:2315: warning: implicit declaration of function ‘SWIG_This’ src/pbs_wrap.c: In function ‘SWIG_Python_SetModule’: src/pbs_wrap.c:2320: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘swig_empty_runtime_method_table’ src/pbs_wrap.c:2320: error: ‘swig_empty_runtime_method_table’ undeclared (first use in this function) src/pbs_wrap.c:2320: error: expected expression before ‘]’ token src/pbs_wrap.c:2322: error: ‘PyObject’ undeclared (first use in this function) src/pbs_wrap.c:2322: error: ‘module’ undeclared (first use in this function) src/pbs_wrap.c:2322: warning: implicit declaration of function ‘Py_InitModule’ src/pbs_wrap.c:2324: error: ‘pointer’ undeclared (first use in this function) src/pbs_wrap.c:2324: warning: implicit declaration of function ‘PyCObject_FromVoidPtr’ src/pbs_wrap.c:2326: warning: implicit declaration of function ‘PyModule_AddObject’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:2333: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c: In function ‘SWIG_Python_TypeQuery’: src/pbs_wrap.c:2342: error: ‘PyObject’ undeclared (first use in this function) src/pbs_wrap.c:2342: error: ‘cache’ undeclared (first use in this function) src/pbs_wrap.c:2342: warning: implicit declaration of function ‘SWIG_Python_TypeCache’ src/pbs_wrap.c:2343: error: ‘key’ undeclared (first use in this function) src/pbs_wrap.c:2343: warning: implicit declaration of function ‘PyString_FromString’ src/pbs_wrap.c:2344: error: ‘obj’ undeclared (first use in this function) src/pbs_wrap.c:2344: warning: implicit declaration of function ‘PyDict_GetItem’ src/pbs_wrap.c:2347: warning: implicit declaration of function ‘PyCObject_AsVoidPtr’ src/pbs_wrap.c:2353: warning: implicit declaration of function ‘PyDict_SetItem’ src/pbs_wrap.c: In function ‘SWIG_Python_AddErrMesg’: src/pbs_wrap.c:2372: error: ‘PyObject’ undeclared (first use in this function) src/pbs_wrap.c:2372: error: ‘type’ undeclared (first use in this function) src/pbs_wrap.c:2373: error: ‘value’ undeclared (first use in this function) src/pbs_wrap.c:2374: error: ‘traceback’ undeclared (first use in this function) src/pbs_wrap.c:2377: error: ‘old_str’ undeclared (first use in this function) src/pbs_wrap.c: In function ‘SWIG_Python_ArgFail’: src/pbs_wrap.c:2399: warning: implicit declaration of function ‘snprintf’ src/pbs_wrap.c:2399: warning: incompatible implicit declaration of built-in function ‘snprintf’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:2407: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2415: error: expected declaration specifiers or ‘...’ before ‘PyObject’ src/pbs_wrap.c: In function ‘SWIG_Python_TypeError’: src/pbs_wrap.c:2429: error: ‘obj’ undeclared (first use in this function) src/pbs_wrap.c:2431: error: ‘PyObject’ undeclared (first use in this function) src/pbs_wrap.c:2431: error: ‘str’ undeclared (first use in this function) src/pbs_wrap.c:2434: error: ‘PyExc_TypeError’ undeclared (first use in this function) src/pbs_wrap.c: At top level: src/pbs_wrap.c:2453: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2499:4: error: #error "This python version requires swig to be run with the '-classic' option" src/pbs_wrap.c:2530: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c: In function ‘get_error’: src/pbs_wrap.c:2636: warning: implicit declaration of function ‘printf’ src/pbs_wrap.c:2636: warning: incompatible implicit declaration of built-in function ‘printf’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:2656: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c: In function ‘SWIG_CanCastAsInteger’: src/pbs_wrap.c:2712: error: ‘errno’ undeclared (first use in this function) src/pbs_wrap.c:2712: error: ‘EDOM’ undeclared (first use in this function) src/pbs_wrap.c:2712: error: ‘ERANGE’ undeclared (first use in this function) src/pbs_wrap.c: At top level: src/pbs_wrap.c:2736: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2775: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2793: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:2813: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:2830: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:2838: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c: In function ‘attrl___str__’: src/pbs_wrap.c:2893: warning: incompatible implicit declaration of built-in function ‘snprintf’ src/pbs_wrap.c: In function ‘delete_attrl’: src/pbs_wrap.c:2900: warning: incompatible implicit declaration of built-in function ‘printf’ src/pbs_wrap.c: In function ‘attropl___str__’: src/pbs_wrap.c:2908: warning: incompatible implicit declaration of built-in function ‘snprintf’ src/pbs_wrap.c: In function ‘delete_attropl’: src/pbs_wrap.c:2915: warning: incompatible implicit declaration of built-in function ‘printf’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:2923: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2967: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2983: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:3008: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3055: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3100: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3146: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3159: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3189: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3236: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3275: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3297: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3336: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3358: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3397: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3419: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3449: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3471: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3493: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3514: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3521: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3551: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3596: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3635: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3657: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3696: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3718: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3757: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3779: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3809: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3831: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3853: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3874: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3881: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3911: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3966: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4005: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4027: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4057: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4104: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4143: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4165: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4172: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:4187: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4195: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:4215: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4223: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4257: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4315: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4413: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4438: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4451: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4464: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4510: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4532: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4554: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4612: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4658: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4774: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4832: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4899: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4957: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5066: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5148: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5179: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5225: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5283: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5341: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5454: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5512: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5578: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5709: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5828: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5959: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6078: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6209: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6319: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6362: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6393: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6424: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6458: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6480: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6502: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6536: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6570: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6595: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6617: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6630: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6643: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6664: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:6679: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6687: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:6702: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6710: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6731: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6776: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6830: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6867: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6921: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6942: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6955: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:6968: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6980: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:7053: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:7078: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:7098: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:7106: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘SwigMethods’ src/pbs_wrap.c:7503: error: expected specifier-qualifier-list before ‘PyObject’ src/pbs_wrap.c:7509: error: expected specifier-qualifier-list before ‘PyObject_HEAD’ src/pbs_wrap.c:7513: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:7518: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:7531: error: expected declaration specifiers or ‘...’ before ‘FILE’ src/pbs_wrap.c: In function ‘swig_varlink_print’: src/pbs_wrap.c:7532: error: ‘PyObject’ undeclared (first use in this function) src/pbs_wrap.c:7532: error: ‘str’ undeclared (first use in this function) src/pbs_wrap.c:7532: warning: implicit declaration of function ‘swig_varlink_str’ src/pbs_wrap.c:7533: warning: implicit declaration of function ‘fprintf’ src/pbs_wrap.c:7533: warning: incompatible implicit declaration of built-in function ‘fprintf’ src/pbs_wrap.c:7533: error: ‘fp’ undeclared (first use in this function) src/pbs_wrap.c: In function ‘swig_varlink_dealloc’: src/pbs_wrap.c:7541: error: ‘swig_varlinkobject’ has no member named ‘vars’ src/pbs_wrap.c:7543: error: ‘swig_globalvar’ has no member named ‘next’ src/pbs_wrap.c:7544: warning: implicit declaration of function ‘free’ src/pbs_wrap.c:7544: warning: incompatible implicit declaration of built-in function ‘free’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:7550: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:7568: error: expected declaration specifiers or ‘...’ before ‘PyObject’ src/pbs_wrap.c: In function ‘swig_varlink_setattr’: src/pbs_wrap.c:7570: error: ‘swig_varlinkobject’ has no member named ‘vars’ src/pbs_wrap.c:7573: error: ‘swig_globalvar’ has no member named ‘set_attr’ src/pbs_wrap.c:7573: error: ‘p’ undeclared (first use in this function) src/pbs_wrap.c:7576: error: ‘swig_globalvar’ has no member named ‘next’ src/pbs_wrap.c:7579: error: ‘PyExc_NameError’ undeclared (first use in this function) src/pbs_wrap.c: At top level: src/pbs_wrap.c:7584: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:7636: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:7646: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:7662: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:7675: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:7702: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c: In function ‘init_pbs’: src/pbs_wrap.c:7755: error: ‘PyObject’ undeclared (first use in this function) src/pbs_wrap.c:7755: error: ‘m’ undeclared (first use in this function) src/pbs_wrap.c:7755: error: ‘d’ undeclared (first use in this function) src/pbs_wrap.c:7755: warning: left-hand operand of comma expression has no effect src/pbs_wrap.c:7758: warning: implicit declaration of function ‘SWIG_Python_FixMethods’ src/pbs_wrap.c:7758: error: ‘SwigMethods’ undeclared (first use in this function) src/pbs_wrap.c:7761: warning: implicit declaration of function ‘PyModule_GetDict’ src/pbs_wrap.c:7764: warning: implicit declaration of function ‘SWIG_Python_InstallConstants’ src/pbs_wrap.c:7767: warning: implicit declaration of function ‘SWIG_Python_SetConstant’ src/pbs_wrap.c:7767: warning: implicit declaration of function ‘SWIG_FromCharPtr’ src/pbs_wrap.c:7966: warning: implicit declaration of function ‘SWIG_From_int’ src/pbs_wrap.c:8036: warning: implicit declaration of function ‘PyDict_SetItemString’ src/pbs_wrap.c:8036: warning: implicit declaration of function ‘SWIG_globals’ src/pbs_wrap.c:8037: warning: implicit declaration of function ‘SWIG_Python_addvarlink’ src/pbs_wrap.c:8037: error: ‘Swig_var_pbs_errno_get’ undeclared (first use in this function) src/pbs_wrap.c:8037: error: ‘Swig_var_pbs_errno_set’ undeclared (first use in this function) src/pbs_wrap.c:8038: error: ‘Swig_var_pbs_server_get’ undeclared (first use in this function) src/pbs_wrap.c:8038: error: ‘Swig_var_pbs_server_set’ undeclared (first use in this function) src/pbs_wrap.c:8048: error: ‘Swig_var_log_event_mask_get’ undeclared (first use in this function) src/pbs_wrap.c:8048: error: ‘Swig_var_log_event_mask_set’ undeclared (first use in this function) src/pbs_wrap.c:8049: error: ‘Swig_var_chk_file_sec_stderr_get’ undeclared (first use in this function) src/pbs_wrap.c:8049: error: ‘Swig_var_chk_file_sec_stderr_set’ undeclared (first use in this function) src/pbs_wrap.c:8050: error: ‘Swig_var_log_buffer_get’ undeclared (first use in this function) src/pbs_wrap.c:8050: error: ‘Swig_var_log_buffer_set’ undeclared (first use in this function) src/pbs_wrap.c:8073: error: ‘Swig_var_msg_daemonname_get’ undeclared (first use in this function) src/pbs_wrap.c:8073: error: ‘Swig_var_msg_daemonname_set’ undeclared (first use in this function) error: command 'gcc' failed with exit status 1 Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/rc/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 57, in scramble self.run_scramble_script() File "/rc/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 206, in run_scramble_script raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) ) galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for pbs_python 4.1.0 Any tips or tricks for a fix would be much appreciated. If it's the only alternative, we could run jobs through DRMAA, though from what I have been reading plenty of issues arise with that as well. Thanks, Frost Mitchell Department of Research Computing Utah State University

2 1

Exit_code not working anymore
by Mathieu Bahin 12 Jul '13

12 Jul '13

Hi all, We have a Galaxy instance that we are regularly keeping up to date following the Galaxy main, so we have the current version (fd4113962c32 commit). For us, since a few updates (unfortunately, I don't know when it started), the "exit_code" tag is not working anymore. I made the simplest tool to confirm : ---------------- <tool id="tool_to_come" name="tool_to_come"> <description></description> <command interpreter="bash"> test.sh $input $output </command> <inputs> <param name="input" type="text" value="7" label="Param" /> </inputs> <outputs> <data name="output" format="fasta" label="Output" /> </outputs> <stdio> <exit_code range="12" level="fatal" description="Grave probleme !" /> </stdio> <help> **Tool documentation** </help> </tool> --------------- #!/bin/bash set -e if [ "$1" -ne 10 ]; then exit 12 else echo "Yeah !" > $2 fi ---------------- Anyway, it still doesn't work as it used to... Am I the only one to have the problem ? Can you help me ? Cheers, Mathieu (Rennes - France)

3 2

Data_ref and multiple selection of columns from input file
by Christos Kannas 12 Jul '13

12 Jul '13

Deal all, We have a tool with the following parameters declarations: <inputs> <param type="data" format="tabular, csv" name="input" required="True" label="Please select the file to read" help = " This tools only supports comma separated (.csv, .txt) and tab separated (.tab, .txt) text files. If you can't see your file in the selection box make sure that you have uploaded it using the correct file format. Alternatively, you can convert almost any character separated text file in to tab separated using the 'Convert delimiters to TAB' tool (under 'Text Manipulation')"/> <param name="idcol" label="Column containing a unique ID for each compound" type="data_column" data_ref="input" accept_default="true" help = "Your file must contain at least one column with a unique ID for each compound."/> <param name="columnList" label="Columns containing property values" type="data_column" data_ref="input" accept_default="true" multiple="true" display="checkboxes" force_select = "false" help = "Your file can contain columns that describe more that one properties. Select all the columns you want to read here."/> <param name="outcol" label="Column containing an outcome value" type="data_column" data_ref="input" accept_default="true" help = "If your file contains a column that describe the outcome of an experiment you should select it here. Currently only one outcome per file is supported."/> </inputs> As you can see in the highlighted lines, we have a parameter that is of type data_column and has data_ref the input dataset, also allows multiple selection. The purpose is to have a multiple selection of columns from the input file. But in the interface we see a '?' as first column and then the columns of the input file. If we remove the multiple select its ok. Does data_ref works along side multiple selection? Regards, Christos -- Christos Kannas Researcher Ph.D Student e-Health Laboratory <http://www.medinfo.cs.ucy.ac.cy/> kannas.christos(a)ucy.ac.cy kannas.christos(a)cs.ucy.ac.cy chriskannas(a)gmail.com Mob: (+357) 99530608

1 1

Trackster and bedtools error
by Perez, Ricardo 12 Jul '13

12 Jul '13

Dear all, As I was trying to do visualize my data set in trackster, I get the following error: /bin/sh: 1: bedtools: not found sort: fflush failed: standard output: Broken pipe sort: write error needLargeMem: trying to allocate 0 bytes (limit: 100000000000) When doing a sudo find / -name "bedtools" in my system, I get the following output: /usr/share/bedtools /usr/share/doc/bedtools Do I have bedtools installed in the wrong place? Thank you for your help, --Ricardo Perez

2 3

Using Jar files in Galaxy
by sridhar srinivasan 12 Jul '13

12 Jul '13

Dear Developers, I am using java jar files for softwares like fastqc, GATK. For running these tools i install the softare and set path in bash_profile file. My doubt is i placed the jar files in galaxy dist folder ( galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc ) is this enough to call the jar files from galaxy?? After placing the jar file i tried running the tool using the interface it gives ERROR as # FastQC cl = /illumina/data/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/illumina/data/galaxy/galaxy-dist/database/job_working_directory/000/216/dataset_546_files --f=bam /illumina/data/galaxy/galaxy-dist/database/job_working_directory/000/216/dataset_546_files/Bowtie2_on_data_7_and_data_6__aligned_reads Exception in thread "main" java.lang.NoClassDefFoundError: uk/ac/babraham/FastQC/FastQCApplication Caused by: java.lang.ClassNotFoundException: uk.ac.babraham.FastQC.FastQCApplication at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) Could not find the main class: uk.ac.babraham.FastQC.FastQCApplication. Program will exit. I got same error for GATK also ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 2.5-2-gf57256b): ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed ##### ERROR Please do not post this error to the GATK forum ##### ERROR ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. ##### ERROR Visit our website and forum for extensive documentation and answers to ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk ##### ERROR ##### ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-a3rr8t) does not exist. ##### ERROR ----------------------------------------------------------------------------------------- Could you please suggest on the same.. Thanks Sridhar

3 3

Tool availability
by vijayalakshmi 11 Jul '13

11 Jul '13

Hi, Are any of the following tools available in galaxy? 1) IDR http://www.uwencode.org/software/hotspot 2) Hotspot https://sites.google.com/site/anshulkundaje/projects/idr 3) Wiggler https://code.google.com/p/align2rawsignal/ 4) PhantomPeakQualTools Regards, Vijayalakshmi.

2 1

Short-term access to a galaxy server for teaching
by Max Heiman 11 Jul '13

11 Jul '13

Hi, We would like to use Galaxy to introduce genomic analysis in our introductory graduate genetics course. Would anyone be willing to let us "borrow" a server for two hours (9-11 am Boston time, Sept 25)? The students will be uploading ~1M 30-bp reads, running QC and trimming barcodes, using BOWTIE to align them to the yeast genome and then MACS to call peaks. There will be about 40 users total. Each task runs quickly on the public server, but we are concerned about the queue times when dealing with a 90-min class. Thank you for any help or advice, best Max

3 2

Config specific tools that auto hide other panels to get more room
by Peng Li 11 Jul '13

11 Jul '13

Dear All I develop one data display tool for my local galaxy instance, I want to make the history panel and tools panel auto hidden while I load this tools since I need more room to show the data, does anyone has any clue for this? Like change the tools xml or add a JS function to operate father web-frame? Many thanks wbflame

2 1