- galaxy-dev - lists.galaxyproject.org

sam_fa_indexes
by Ryan Davis 13 Jul '13

13 Jul '13

Hi, We have just installed a local Galaxy instance on a workstation and I am having issues getting references to show up for my samtools section. I have setup many.loc files correctly for my other tools and I am able to see and use them in Galaxy. In the paster.log I see the following: galaxy.tools.data WARNING 2013-07-10 17:05:06,034 Line 30 in tool data table 'sam_fa_indexes' is invalid (HINT: '<TAB>' characters must be used to separate fields): index hg19 /mnt/data3/Reference/human/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/ genome.fa galaxy.tools.data WARNING 2013-07-10 17:05:06,034 Line 31 in tool data table 'sam_fa_indexes' is invalid (HINT: '<TAB>' characters must be used to separate fields): index mm10 /mnt/data3/Reference/mouse/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/ genome.fa galaxy.tools.data DEBUG 2013-07-10 17:05:06,034 Loaded tool data table 'sam_fa_indexes' I know for a fact that when I first created this file I had a space (not a TAB) in between index and the build. After restarting the Galaxy service several times and double checking our loc files I noticed the error and replace the space with a TAB. Using vi (with :set list) we see that there are TABs in between the fields. #index^Ihg18^I/depot/data2/galaxy/sam/hg18.fa$ #index^Ihg19^I/depot/data2/galaxy/sam/hg19.fa$ index^Ihg19^I/mnt/data3/Reference/human/Homo_sapiens/UCSC/hg19/Sequence/sam/ hg19.fa$ index^Imm10^I/mnt/data3/Reference/mouse/Mus_musculus/UCSC/mm10/Sequence/sam/ mm10.fa$ Even with the correct file, I still get the same error in the paster.log. Does this get saved in the database? How do I resolve this? Thanks for the help! Ryan

1 0

Dynamically decide where a Galaxy tool runs
by Saliya Ekanayake 12 Jul '13

12 Jul '13

Hi, I see in documentation that Galaxy tools may be configured to run on a cluster (http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster<http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#DRMAA>). This is something our research group is interested in, but it's not possible to specify which cluster the particular tool should run on ahead of time. Therefore, is it possible to specify the cluster to run when the tool is actually being used when composing the workflow from Galaxy? Thank you, Saliya -- Saliya Ekanayake esaliya(a)gmail.com Cell 812-391-4914 Home 812-961-6383 http://saliya.org

3 4

BWA - failed to resolve dependency error
by Shantanu Pavgi (Campus) 12 Jul '13

12 Jul '13

I had migrated BWA tool while at release_2013.02.08 revision. It was working fine, however, it fails to run with following warning message after updating Galaxy to release_2013.06.03. {{{ Building dependency shell command for dependency 'bwa' galaxy.tools WARNING 2013-07-11 17:16:28,429 Failed to resolve dependency on 'bwa', ignoring }}} The bwa tool dependency is installed and present on the system. I am not sure why it's not being detected after the update. I can fix it by sourcing env.sh file before starting Galaxy server process, but that's not a good solution. Any pointers on resolving this issue would be really helpful. Also, Galaxy is unable to fetch latest update for the bwa_wrapper. The migration script had installed first release of the bwa_wrapper, but now there is an updated revision available. I tried getting updates, but Galaxy thinks it's current bwa revision is up to date. -- Thanks, Shantanu

1 1

Lessen load on server
by Auerbach, Kenneth R. 12 Jul '13

12 Jul '13

Hello, Can you tell me if there is any way to lessen the load of Galaxy on our server. Even when it's idle it's consuming a lot of resources. Thank you. Ken. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

2 1

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)

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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

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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

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