- galaxy-dev - lists.galaxyproject.org

Additional Information about users in the API
by Milen Kouylekov 25 Apr '17

25 Apr '17

Dear Team, Hi, my name is Milen Kouylekov and I am working on the galaxy portal customized for natural language technology applications. http://lap.clarino.uio.no. I wrote an reporting script that uses Galaxy API to summarize the user activity. The idea of the script is to send regular reports with the information available to the reporting server as well as additional information like queries that failed to execute etc. I have managed to retrieve using the API most of the relevant information except the following: 1) User creation date. 2) User last access date. I have investigated that user object and see that information is part of it. My question is: Is there a way to access this information through the API? If not can I make a feature request? It is an information useful for administration of a galaxy instance. Cheers Milen

3 4

Galaxy User IDs and Group IDs
by Lemley, Rob 24 Apr '17

24 Apr '17

Hi everyone, This may seem like a silly question, but are user id's and group id's expected to be the "same"? For example: >>> gi.users.get_users() [{u'username': u'user1', u'model_class': u'User', u'id': u'f2db41e1fa331b3e', u'email': u'XXXXX'}, {u'username': u'user2', u'model_class': u'User', u'id': u'f597429621d6eb2b', u'email': u'XXXXX'}] >>> gi.groups.get_groups() [{u'url': u'/api/groups/f2db41e1fa331b3e', u'model_class': u'Group', u'id': u'f2db41e1fa331b3e', u'name': u'group1'}, {u'url': u'/api/groups/f597429621d6eb2b', u'model_class': u'Group', u'id': u'f597429621d6eb2b', u'name': u'group2'}] This is just a dev instance I set up really quick, so these are the first two users/groups I've created. If this is expected behavior I'll carry on, just seems odd to me. Thanks! -Rob -- Rob Lemley Systems Administrator - CIRC University of Rochester

2 1

conda path problem
by Matthias Bernt 20 Apr '17

20 Apr '17

Dear list, now that I got conda working I got a new error when installing tools (bot when installing via the web interface and via the galaxy-tools ansible role). There seems to be an update write on a nonexistent file ...../_condarc I guess an important point is that I needed to redefine the conda path in galaxy.ini (since I got warnings that the path name was to long). Maybe there are still some hard coded paths around? Best, Matthias Uncaught exception in exposed API method: Traceback (most recent call last): File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/decorators.py", line 282, in decorator rval = func( self, trans, *args, **kwargs ) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py", line 502, in install_repository_revision payload ) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/tool_shed/galaxy_install/install_manager.py", line 706, in install install_options File "/gpfs1/data/galaxy_server/galaxy-dev/lib/tool_shed/galaxy_install/install_manager.py", line 805, in __initiate_and_install_repositories return self.install_repositories(tsr_ids, decoded_kwd, reinstalling=False) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/tool_shed/galaxy_install/install_manager.py", line 852, in install_repositories tool_panel_section_mapping=tool_panel_section_mapping ) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/tool_shed/galaxy_install/install_manager.py", line 910, in install_tool_shed_repository [self._view.install_dependencies(r) for r in new_requirements] File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/views.py", line 59, in install_dependencies return self._dependency_manager._requirements_to_dependencies_dict(requirements, **{'install': True}) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/__init__.py", line 148, in _requirements_to_dependencies_dict dependencies = resolver.resolve_all(resolvable_requirements, **kwds) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/resolvers/conda.py", line 171, in resolve_all is_installed = self.install_all(conda_targets) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/resolvers/conda.py", line 126, in install_all return_code = install_conda_targets(conda_targets, env, conda_context=self.conda_context) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/conda_util.py", line 405, in install_conda_targets conda_context.ensure_channels_configured() File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/conda_util.py", line 136, in ensure_channels_configured self.save_condarc(conda_conf) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/conda_util.py", line 198, in save_condarc raise Exception(message) Exception: Failed to update write to path [/gpfs1/data/galaxy_server/galaxy-dev/database/dependencies/_condarc] while attempting to update conda configuration, please update the configuration to override the condarc location or grant this application write to the parent directory. -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

1 0

conda installation fails
by Matthias Bernt 20 Apr '17

20 Apr '17

Dear list, Just found out that conda is not installing on our CentOS6.8 installation (might be related to earlier messages). The problem is that the shell script installing conda unsets the LD_LIBRARY_PATH which makes tar dysfunctional (tar is called by the installer). The command line that is executed during galaxy's installation is wget -q --recursive -O '/tmp/conda_install7tWo7r.sh' 'https://repo.continuum.io/miniconda/Miniconda3-4.2.12-Linux-x86_64.sh' && bash '/tmp/conda_install7tWo7r.sh' -b -p '/gpfs1/data/galaxy_server/galaxy-dev/_conda' && /gpfs1/data/galaxy_server/galaxy-dev/_conda/bin/conda install -y -q conda=4.2.13 Removing the unset LD_LIBRARY_PATH line (and fiddling around with some file size checks) is (seemingly) successful. There is an open issue on the conda github: https://github.com/conda/conda/issues/3632 Any suggestions? The line removal procedure seems to be quite complicated in an automated ansible installation which I try to achieve. Cheers, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

3 3

GCC2107 Oral presentation abstract deadline extended to 29 April
by Dave Clements 19 Apr '17

19 Apr '17

Hello all, The deadline for submitting oral presentation abstracts for the 2017 Galaxy Community Conference <https://gcc2017.sciencesconf.org/> has been extended to 29 April. And a reminder of some other GCC2017 <https://gcc2017.sciencesconf.org/> deadlines: 15 May: Early registration <https://gcc2017.sciencesconf.org/page/registration> ends 27 May: Poster presentation abstracts <https://gcc2017.sciencesconf.org/page/submit> are due. 27 May: Visualization and Computer Demo presentation abstracts <https://gcc2017.sciencesconf.org/page/submit> are due. 31 May: Regular registration <https://gcc2017.sciencesconf.org/page/registration> ends 23 June: Lightning Talk presentation abstracts <https://gcc2017.sciencesconf.org/page/submit> are due. *About GCC2017:* GCC2017 will be in Montpellier, France, 26-30 June and will feature two days of presentations, discussions, poster sessions, lightning talks, computer demos, keynotes, and birds-of-a-feather meetups, all about data-intensive biology and the tools that support it. GCC2017 also includes data and coding hackathons <https://gcc2017.sciencesconf.org/page/hackathon>, and two days of training <https://gcc2017.sched.com/overview/type/Training> covering 16 different topics. GCC2017 will be held at Le Corum Conference Centre <http://www.montpellier-events.com/en/The-Corum/Presentation> in the heart of Montpellier <https://gcc2017.sciencesconf.org/page/location>, just 10km from the Mediterranean. This event will gather several hundred researchers addressing diverse questions and facing common challenges in data intensive life science research. GCC participants work across the tree of life, come from around the world, and work at universities, research organizations, industry, medical schools and research hospitals. If you work in or support data intensive life science research then GCC2017 is an ideal opportunity to present your work. Early registration <https://gcc2017.sciencesconf.org/page/registration> is starts at less than 55€ / day for post-docs and students. You can also book low cost conference housing <https://gcc2017.sciencesconf.org/page/lodging> when you register. GCC2017 has sold out *all* premiere *sponsorship* <https://gcc2017.sciencesconf.org/page/sponsors> slots (a first). If you are interested in sponsoring (or know someone who is) there are still Silver and Bronze and Hackathon sponsorships available. Contact the organisers if you are interested. About Galaxy Galaxy <https://galaxyproject.org/> is an open, web-based platform for data-intensive biomedical analysis used by tens of thousands of researchers around the world. It supports ad hoc exploration and analysis through scalable and repeatable data analysis pipelines for large research studies. Galaxy is available in over 90 free and publicly accessible web servers, on commercial and national cloud infrastructures, and is locally installed at hundreds, if not thousands, of research organisations around the world. We hope to see you this summer in Montpellier! Au revoir, The GCC2017 Organising Committee -- https://galaxyproject.org/ https://getgalaxy.org/ https://usegalaxy.org/ https://gcc2017.sciencesconf.org/

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atlas version 3.10.2 installation error
by Matthias Bernt 19 Apr '17

19 Apr '17

Dear list, again me :( stumbling from problem to problem ... I got compilation errors when installing package_atlas_3_10 Revision: 98c017ec230d I tried with gcc 4x and 6x without success. Do I need the intel C compiler for this tool? If I got earlier posts (http://dev.list.galaxyproject.org/atlas-3-10-IUC-error-tt4668236.html) correct a precompiled version should be used anyway? I'm running galaxy on CentOS 6.8 (64bit) (running in a VirtualBox). Best, Matthias Here is the output (which I guess is verbose output from configure): /tmp/cctyMGAH.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' probe_OS.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' probe_asm.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' system(make IRun_GAS_x8632 args="-v 2" MYFLAGS="-DATL_OS_Linux" 2> /dev/null | fgrep SUCCESS) ierr=256 in command='make IRun_GAS_x8632 args="-v 2" MYFLAGS="-DATL_OS_Linux" 2> /dev/null | fgrep SUCCESS'! OUTPUT: ======= system(make IRun_GAS_x8664 args="-v 2" MYFLAGS="-DATL_OS_Linux" 2> /dev/null | fgrep SUCCESS) probe_vec.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' ierr=256 in command='make IRun_VSX MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'! OUTPUT: ======= ierr=256 in command='make IRun_AltiVec MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'! OUTPUT: ======= ierr=256 in command='make IRun_AVXFMA4 MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'! OUTPUT: ======= ierr=256 in command='make IRun_3DNow MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'! OUTPUT: ======= ierr=256 in command='make IRun_NEON MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'! OUTPUT: ======= probe_arch.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' /tmp/cc8hbxc1.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' ERROR: enum fam=3, chip=2, model=79, mach=0 make[3]: *** [atlas_run] Error 44 make[2]: *** [IRunArchInfo_x86] Error 2 /tmp/ccafA8Bi.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' ERROR: enum fam=3, chip=2, model=79, mach=0 make[3]: *** [atlas_run] Error 44 make[2]: *** [IRunArchInfo_x86] Error 2 ERROR: enum fam=3, chip=2, model=79, mach=0 make[3]: *** [atlas_run] Error 44 make[2]: *** [IRunArchInfo_x86] Error 2 cmnd='make IRun_comp args="-v 2 -o atlconf.txt -O 1 -A 39 -Si nof77 0 -V 488 -Fa ic '-fPIC' -Fa sm '-fPIC' -Fa dm '-fPIC' -Fa sk '-fPIC' -Fa dk '-fPIC' -Fa xc '-fPIC' -Fa gc '-fPIC' -Fa if '-fPIC' -b 64"' /tmp/cc8W8Itx.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' probe_comp.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' ierr=256 in command='find /gpfs1/data/galaxy_server/galaxy-dev/.venv/bin /usr/local/gcc/6.2.0-1/bin /global/apps/bioinf/galaxy/bin/Python-2.7.13/bin /usr/local/sqlite/3.15.1-1/bin /global/apps/bioinf/galaxy/bin/postgresql-9.6.2/bin /usr/local/git/2.10.1-1/bin /usr/local/pcre/8.38-1/bin /usr/local/ncurses/5.9-1/bin /usr/local/bzip2/1.0.6-3/bin /usr/local/expat/2.1.1-1/bin /usr/local/curl/7.41.0-1/bin /usr/local/openssl/1.0.2-1/usr/bin /usr/local/uge/8.4.4-1/bin/lx-amd64 /usr/local/bin /bin /usr/bin /usr/local/sbin /usr/sbin /sbin /home/songalax/bin -maxdepth 1 -name '*gcc*' -exec ./xisgcc '{}' \;'! OUTPUT: ======= cmnd=make IRunCComp CC='/usr/local/gcc/6.2.0-1/bin/gcc' CCFLAGS='-O' | fgrep SUCCESS /usr/local/gcc/6.2.0-1/bin/gcc -O : SUCCESS! cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O' | fgrep SUCCESS /usr/bin/gcc -O : SUCCESS! sh: -c: line 0: unexpected EOF while looking for matching ``' sh: -c: line 1: syntax error: unexpected end of file ierr=256 in command='find $HOME/local -name '*gcc*' -exec ./xisgcc '{}' \;'! OUTPUT: ======= cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O' | fgrep SUCCESS /usr/bin/gcc -O : SUCCESS! sh: -c: line 0: unexpected EOF while looking for matching ``' sh: -c: line 1: syntax error: unexpected end of file ierr=256 in command='find /usr/local /bin /sbin /usr/bin /usr/sbin /opt/bin /opt/sbin -name '*gcc*' -exec ./xisgcc '{}' \;'! OUTPUT: ======= cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O' | fgrep SUCCESS /usr/bin/gcc -O : SUCCESS! sh: -c: line 0: unexpected EOF while looking for matching ``' sh: -c: line 1: syntax error: unexpected end of file sh: -c: line 0: unexpected EOF while looking for matching ``' sh: -c: line 1: syntax error: unexpected end of file Compiler nodes: Fresh Read 0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77' '-O' 1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77' '-O' 2. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran' '-O' 3. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc' '-O -fomit-frame-pointer' 4. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-mcpu=cortex-a8 -mfpu=vfpv3 -mfloat-abi=softfp -O' 5. priority=1000, comps,OS,arch[0]=(20,1,0), comp='gcc' '-O1 -mcpu=cortex-a8 -mtune=cortex-a8 -mfpu=vfpv3 -mfloat-abi=softfp -fno-schedule-insns2' 6. priority=1000, comps,OS,arch[0]=(75,1,0), comp='gcc' '-O1 -mcpu=cortex-a8 -mtune=cortex-a8 -mfpu=vfpv3 -mfloat-abi=softfp -fno-expensive-optimizations' 7. priority=1000, comps,OS,arch[0]=(32,1,0), comp='gcc' '-mcpu=cortex-a8 -O1 -mfpu=vfpv3 -mfloat-abi=softfp ' 8. priority=0, comps,OS,arch[0]=(63,768,1075838976), comp='icl' '-QxN -O3 -Qprec -fp:extended -fp:except -nologo -Oy' 9. priority=0, comps,OS,arch[0]=(128,768,1), comp='ifort' '-O2 -fltconsistency -nologo' 10. priority=0, comps,OS,arch[0]=(63,768,1), comp='cl' '-Oy -Ox -arch:SSE2 -nologo' 11. priority=4, comps,OS,arch[0]=(63,768,1048576), comp='cl' '-Oy -Ox -arch:SSE -nologo' 12. priority=4, comps,OS,arch[0]=(63,768,983040), comp='cl' '-Oy -Ox' 13. priority=500, comps,OS,arch[0]=(127,1,3584), comp='gcc' '-O3 -funroll-loops' 14. priority=500, comps,OS,arch[0]=(128,1,3584), comp='gfortran' '-O3 -funroll-loops' 15. priority=600, comps,OS,arch[0]=(128,1,2048), comp='gfortran' '-march=z9-109 -O3 -funroll-loops' 16. priority=600, comps,OS,arch[0]=(127,1,2048), comp='gcc' '-march=z9-109 -O3 -funroll-loops' 17. priority=800, comps,OS,arch[0]=(128,1,2048), comp='gfortran' '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays' 18. priority=800, comps,OS,arch[0]=(127,1,2048), comp='gcc' '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays' 19. priority=1000, comps,OS,arch[0]=(127,1,2048), comp='gcc' '-march=z196 -O3 -funroll-loops -fno-prefetch-loop-arrays' 20. priority=1000, comps,OS,arch[0]=(128,1,2048), comp='gfortran' '-march=z196 -O3 -funroll-loops -fno-prefetch-loop-arrays' 21. priority=600, comps,OS,arch[0]=(127,1,1024), comp='gcc' '-march=z9-109 -O3 -funroll-loops -fno-prefetch-loop-arrays' 22. priority=600, comps,OS,arch[0]=(128,1,1024), comp='gfortran' '-march=z9-109 -O3 -funroll-loops' 23. priority=1000, comps,OS,arch[0]=(127,1,1024), comp='gcc' '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays' 24. priority=1000, comps,OS,arch[0]=(127,1,512), comp='gcc' '-march=z9-109 -O3 -funroll-loops' 25. priority=1010, comps,OS,arch[0]=(128,1,4), comp='xlf' '-qtune=pwr4 -qarch=pwr4 -O3 -qmaxmem=-1 -qfloat=hsflt' 26. priority=1010, comps,OS,arch[0]=(127,1,4), comp='gcc' '-mcpu=power4 -mtune=power4 -O3 -fno-schedule-insns -fno-rerun-loop-opt' 27. priority=1010, comps,OS,arch[0]=(128,1,8), comp='xlf' '-qtune=pwr5 -qarch=pwr5 -O3 -qmaxmem=-1 -qfloat=hsflt' 28. priority=1010, comps,OS,arch[0]=(128,1,128), comp='xlf' '-qtune=pwr7 -qarch=pwr7 -O3 -qmaxmem=-1 -qfloat=hsflt' 29. priority=1010, comps,OS,arch[0]=(128,1,8), comp='gfortran' '-mcpu=power5 -mtune=power5 -O3 -fno-schedule-insns -fno-rerun-loop-opt' 30. priority=1010, comps,OS,arch[0]=(128,1,64), comp='gfortran' '-mcpu=power6 -mtune=power6 -maltivec -O3 -fno-schedule-insns -fschedule-insns2 -minsert-sched-nops=2' 31. priority=1010, comps,OS,arch[0]=(127,1,8), comp='gcc' '-mcpu=power5 -mtune=power5 -O3 -fno-schedule-insns -fno-rerun-loop-opt' 32. priority=1010, comps,OS,arch[0]=(127,1,64), comp='gcc' '-mcpu=power6 -mtune=power6 -maltivec -O3 -fno-schedule-insns -fschedule-insns2 -minsert-sched-nops=2' 33. priority=1010, comps,OS,arch[0]=(128,1,128), comp='gfortran' '-O2 -mvsx -mcpu=power7 -mtune=power7 -m64 -mvrsave -funroll-all-loops' 34. priority=1010, comps,OS,arch[0]=(127,1,128), comp='gcc' '-O2 -mvsx -mcpu=power7 -mtune=power7 -m64 -mvrsave -funroll-all-loops' 35. priority=1000, comps,OS,arch[0]=(8,1,32), comp='gcc' '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -O2 -mvrsave' 36. priority=1000, comps,OS,arch[0]=(117,1,32), comp='gcc' '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -O2' 37. priority=1000, comps,OS,arch[0]=(2,1,32), comp='gcc' '-Os -mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -mvrsave -fno-schedule-insns2 -fno-schedule-insns' 38. priority=1000, comps,OS,arch[0]=(121,1,16), comp='gcc' '-O3 -maltivec -mabi=altivec -mcpu=7400 -mtune=7400 -fno-schedule-insns -fschedule-insns2' 39. priority=1000, comps,OS,arch[0]=(2,1,16), comp='gcc' '-Os -maltivec -mabi=altivec -mcpu=7400 -mtune=7400' 40. priority=1000, comps,OS,arch[0]=(4,1,16), comp='gcc' '-Os -maltivec -mabi=altivec -mcpu=7400 -mtune=7400' 41. priority=1, comps,OS,arch[0]=(33,1,0), comp='pathcc' '-march=auto -O2 -OPT:Olimit=15000 -LNO:blocking=OFF' 42. priority=1, comps,OS,arch[0]=(6,1,0), comp='pathcc' '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed -march=auto -LNO:opt=0 -LNO:full_unroll_outer=OFF -LNO:fusion=0 -LNO:prefetch=2' 43. priority=1, comps,OS,arch[0]=(24,1,0), comp='pathcc' '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed -march=auto' 44. priority=1000, comps,OS,arch[0]=(128,1,0), comp='pathf95' '-march=auto -O2' 45. priority=500, comps,OS,arch[0]=(127,1,0), comp='gcc' '-O2 -mips64 -march=5kf -mtune=5kf -fno-schedule-insns -fschedule-insns2 -fno-peephole -fno-peephole2' 46. priority=1000, comps,OS,arch[0]=(128,32,0), comp='f77' '-O2' 47. priority=1000, comps,OS,arch[0]=(97,32,0), comp='cc' '-O2 -OPT:Olimit=15000 -LNO:blocking=OFF' 48. priority=1000, comps,OS,arch[0]=(30,32,0), comp='cc' '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed' 49. priority=1010, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-fomit-frame-pointer -O2 -fno-tree-loop-optimize' 50. priority=1000, comps,OS,arch[0]=(30,1,0), comp='gcc' '-fomit-frame-pointer -O2' 51. priority=1010, comps,OS,arch[0]=(30,1,0), comp='gcc' '-fomit-frame-pointer -O2 -fno-tree-loop-optimize' 52. priority=10, comps,OS,arch[0]=(128,1,0), comp='g77' '-O -mcpu=ultrasparc3 -mtune=ultrasparc3' 53. priority=100, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-O -mcpu=ultrasparc3 -mtune=ultrasparc3' 54. priority=1000, comps,OS,arch[0]=(128,1,0), comp='f77' '-dalign -native -xO5' 55. priority=1000, comps,OS,arch[0]=(96,1,0), comp='gcc' '-mcpu=ultrasparc3 -mtune=ultrasparc3 -O' 56. priority=1000, comps,OS,arch[0]=(29,1,0), comp='gcc' '-O3 -mcpu=ultrasparc3 -mtune=ultrasparc3 -fno-schedule-insns2 -fschedule-insns' 57. priority=1000, comps,OS,arch[0]=(2,1,0), comp='gcc' '-O1 -mcpu=ultrasparc3 -mtune=ultrasparc3 -fschedule-insns -fmodulo-sched' 58. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-mcpu=niagara2 -mtune=niagara2 -Os' 59. priority=1000, comps,OS,arch[0]=(127,1,0), comp='gcc' '-mcpu=niagara2 -mtune=niagara2 -Os' 60. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -mfma4 -O2 -fno-tree-loop-optimize' 61. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' '-Os -fomit-frame-pointer' 62. priority=1005, comps,OS,arch[0]=(95,896,0), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 63. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 64. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-fomit-frame-pointer -mfpmath=sse -O2' 65. priority=1000, comps,OS,arch[0]=(95,1,12582912), comp='gcc' '-fomit-frame-pointer -O3 -mfpmath=387' 66. priority=1005, comps,OS,arch[0]=(31,896,12582912), comp='gcc-4' '-fomit-frame-pointer -O3 -mfpmath=387' 67. priority=1000, comps,OS,arch[0]=(95,1,-1071906816), comp='gcc' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 68. priority=1005, comps,OS,arch[0]=(31,896,1835008), comp='gcc-4' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 69. priority=1000, comps,OS,arch[0]=(128,1,1835008), comp='gfortran' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 70. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' '-fomit-frame-pointer -mfpmath=387 -O2' 71. priority=1005, comps,OS,arch[0]=(31,896,0), comp='gcc-4' '-fomit-frame-pointer -mfpmath=387 -O2' 72. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-fomit-frame-pointer -mfpmath=387 -O2' 73. priority=1000, comps,OS,arch[0]=(25,1,-1073741824), comp='gcc-4' '-O2 -fomit-frame-pointer -mfpmath=sse' 74. priority=1005, comps,OS,arch[0]=(6,896,-1073741824), comp='gcc-4' '-O2 -fomit-frame-pointer -mfpmath=sse -fno-schedule-insns -fno-optimize-register-move' 75. priority=1000, comps,OS,arch[0]=(6,1,-1073741824), comp='gcc' '-O2 -fomit-frame-pointer -mfpmath=sse -fno-schedule-insns -fno-optimize-register-move' 76. priority=1000, comps,OS,arch[0]=(25,1,-2147483648), comp='gcc' '-O2 -fomit-frame-pointer -mfpmath=sse' 77. priority=1000, comps,OS,arch[0]=(128,1,-1073741824), comp='gfortran' '-O2 -fomit-frame-pointer -mfpmath=sse' 78. priority=1000, comps,OS,arch[0]=(128,1,32768), comp='gfortran' '-fomit-frame-pointer -mfpmath=sse -O2' 79. priority=1000, comps,OS,arch[0]=(95,1,32768), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 80. priority=1000, comps,OS,arch[0]=(128,1,16384), comp='gfortran' '-fomit-frame-pointer -mfpmath=sse -O2' 81. priority=1000, comps,OS,arch[0]=(95,1,16384), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 82. priority=1000, comps,OS,arch[0]=(128,1,8192), comp='gfortran' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 83. priority=1000, comps,OS,arch[0]=(10,1,8192), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 84. priority=1000, comps,OS,arch[0]=(85,1,8192), comp='gcc' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 85. priority=1000, comps,OS,arch[0]=(128,1,12288), comp='gfortran' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 86. priority=1000, comps,OS,arch[0]=(95,1,4096), comp='gcc' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 87. priority=1000, comps,OS,arch[0]=(65,1,536870912), comp='gcc' '-O' 88. priority=1000, comps,OS,arch[0]=(30,1,536870912), comp='gcc' '-O3 -fno-schedule-insns2 -funroll-all-loops -fno-tree-ch' 89. priority=1000, comps,OS,arch[0]=(95,1,33554432), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 90. priority=1005, comps,OS,arch[0]=(31,896,33554432), comp='gcc-4' '-fomit-frame-pointer -mfpmath=sse -O2' 91. priority=1000, comps,OS,arch[0]=(95,1,67108864), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 92. priority=1005, comps,OS,arch[0]=(95,896,67108864), comp='gcc-4' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 93. priority=50, comps,OS,arch[0]=(57,1,134217728), comp='clang' '-fomit-frame-pointer -mavx -O2 -m64 -Wno-parentheses' 94. priority=1000, comps,OS,arch[0]=(127,1,134217728), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 95. priority=1005, comps,OS,arch[0]=(31,896,134217728), comp='gcc-4' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 96. priority=1000, comps,OS,arch[0]=(127,1,268435456), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' Compiler nodes: Targeted 0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77' '-O' 1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77' '-O' 2. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran' '-O' 3. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc' '-O -fomit-frame-pointer' Compiler nodes: Sorted 0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77' '-O' 1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77' '-O' 2. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc' '-O -fomit-frame-pointer' 3. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran' '-O' cc1: error: unrecognized command line option "-mavx2" make[2]: *** [IRunCComp] Error 1 ierr=256 in command='make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O -fomit-frame-pointer -mavx2 -mfma -fPIC -m64' | fgrep SUCCESS'! OUTPUT: ======= cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O -fomit-frame-pointer -mavx2 -mfma -fPIC -m64' | fgrep SUCCESS /usr/bin/gcc -O -fomit-frame-pointer -mavx2 -mfma -fPIC -m64 : FAILURE! Unable to find usable compiler for ICC; abortingMake sure compilers are in your path, and specify good compilers to configure (see INSTALL.txt or 'configure --help' for details)make[1]: *** [atlas_run] Error 1 make: *** [IRun_comp] Error 2 ERROR 512 IN SYSCMND: 'make IRun_comp args="-v 2 -o atlconf.txt -O 1 -A 39 -Si nof77 0 -V 488 -Fa ic '-fPIC' -Fa sm '-fPIC' -Fa dm '-fPIC' -Fa sk '-fPIC' -Fa dk '-fPIC' -Fa xc '-fPIC' -Fa gc '-fPIC' -Fa if '-fPIC' -b 64"' Make.top:1: Make.inc: No such file or directory Make.top:329: warning: overriding commands for target `/AtlasTest' Make.top:80: warning: ignoring old commands for target `/AtlasTest' make[1]: *** No rule to make target `Make.inc'. Stop. make: *** [startup] Error 2 mv: cannot stat `lib/Makefile': No such file or directory ../configure: line 450: lib/Makefile: No such file or directory ../configure: line 451: lib/Makefile: No such file or directory ../configure: line 452: lib/Makefile: No such file or directory ../configure: line 453: lib/Makefile: No such file or directory ../configure: line 509: lib/Makefile: No such file or directory Make.top:1: Make.inc: No such file or directory Make.top:329: warning: overriding commands for target `/AtlasTest' Make.top:80: warning: ignoring old commands for target `/AtlasTest' make[1]: *** No rule to make target `Make.inc'. Stop. make: *** [build] Error 2 -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

3 8

Testing updated NCBI BLAST+ wrappers for version 2.5.0
by Peter Cock 19 Apr '17

19 Apr '17

Hello all, I have updated the NCBI BLAST+ wrappers on the Test Tool Shed, the wrapper is now at v0.2.00: https://testtoolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ The main changes is this now depends on BLAST+ 2.5.0, and that is available via either BioConda or the Tool Shed: https://toolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_5_0/ https://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_5_0/ In order for the dependency to work smoothly on both BioConda and the Tool Shed system, we have changed the package name from "blast+" to just "blast". Given the NCBI stopped updated the original "legacy" BLAST some time ago, when combined with the version number this is no longer ambiguous. Jumping from using BLAST+ 2.2.31 to using BLAST+ 2.5.0 required updating lots of the test files for NCBI changes, including dropping the GI numbers in many outputs, expanding the percentage identity field from 2dp to 3dp, and also changing how -parse_deflines works with tabular output. The wrappers (deliberately) do not yet offer any new functionality added in the recent NCBI BLAST+ updates, in particular BLAST XML v2 is not yet available as an output with a datatype in Galaxy. At this point I would welcome feedback from those of you using the BLAST+ wrappers - including if you were able to install this with the dependencies from BioConda or the traditional Tool Shed packages. Once I'm confident that this is all OK, I will update the main Tool Shed (and think about adding new functionality in 2017). Thank you all, Peter

1 1

SSL certificate errors
by Matthias Bernt 18 Apr '17

18 Apr '17

Dear list, Currently I get SSL certificate errors when I try to install a tool in Galaxy. I also get the same error when I try to use the galaxy-tools ansible role (when debugging this I thought this might be because my local server is on http, since the error appeared seemingly when a message was posted to the local server -- but I'm not entirely sure). I'm also missing the "Manage installed tools" link in the admin area (but maybe this is expected in a fresh install?). Thanks a lot. Best, Matthias This is the stack trace when I try to install through the web frontend: 141.65.27.89 - - [18/Apr/2017:14:58:19 +0000] "GET /admin_toolshed/prepare_for_install?changeset_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d2070513e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 500 - "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:52.0) Gecko/20100101 Firefox/52.0" Error - <class 'urllib2.URLError'>: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)> URL: http://bioinf2-dev:8080/admin_toolshed/prepare_for_install?changeset_revisi… File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/middleware/error.py', line 154 in __call__ app_iter = self.application(environ, sr_checker) File '/gpfs1/data/galaxy_server/galaxy-dev/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/gpfs1/data/galaxy_server/galaxy-dev/.venv/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/base.py', line 134 in __call__ return self.handle_request( environ, start_response ) File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/base.py', line 193 in handle_request body = method( trans, **kwargs ) File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/decorators.py', line 98 in decorator return func( self, trans, *args, **kwargs ) File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1035 in prepare_for_install raw_text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params ) File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/util/__init__.py', line 1488 in url_get response = urlopener.open( full_url ) File '/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/urllib2.py', line 429 in open response = self._open(req, data) File '/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/urllib2.py', line 447 in _open '_open', req) File '/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/urllib2.py', line 407 in _call_chain result = func(*args) File '/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/urllib2.py', line 1241 in https_open context=self._context) File '/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/urllib2.py', line 1198 in do_open raise URLError(err) URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)> CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5' HTTP_CONNECTION: 'keep-alive' HTTP_COOKIE: 'galaxysession=5d9fe20b2f75201eeee9486487f5942375617bcc89a7da2cc7e5bd9aff8a0eb130e333f3419e10fa' HTTP_DNT: '1' HTTP_HOST: 'bioinf2-dev:8080' HTTP_UPGRADE_INSECURE_REQUESTS: '1' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:52.0) Gecko/20100101 Firefox/52.0' PATH_INFO: '/admin_toolshed/prepare_for_install' QUERY_STRING: 'changeset_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d2070513e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F' REMOTE_ADDR: '141.65.27.89' REQUEST_METHOD: 'GET' SERVER_NAME: '0.0.0.0' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.1' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x7f2dd8bb5190> controller_action_key: u'web.admin_toolshed.prepare_for_install' is_api_request: False paste.cookies: (<SimpleCookie: galaxysession='5d9fe20b2f75201eeee9486487f5942375617bcc89a7da2cc7e5bd9aff8a0eb130e333f3419e10fa'>, 'galaxysession=5d9fe20b2f75201eeee9486487f5942375617bcc89a7da2cc7e5bd9aff8a0eb130e333f3419e10fa') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x7f2dd8bb5110> paste.httpserver.proxy.host: 'dummy' paste.httpserver.proxy.scheme: 'http' paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x7f2dd875fe10> paste.parsed_querystring: ([('changeset_revisions', '9ba8ebb636f4'), ('repository_ids', 'd5dd1c5d2070513e'), ('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/')], 'changeset_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d2070513e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F') paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True request_id: '7599ea98244711e7941208002755efa5' webob._parsed_query_vars: (GET([(u'changeset_revisions', u'9ba8ebb636f4'), (u'repository_ids', u'd5dd1c5d2070513e'), (u'tool_shed_url', u'https://toolshed.g2.bx.psu.edu/')]), 'changeset_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d2070513e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F') wsgi process: 'Multithreaded' ------------------------------------------------------------ -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

2 2

GCC2107 Update: Oral presentation abstracts due 15 April
by Dave Clements 13 Apr '17

13 Apr '17

Hello all, This is just a reminder of some *GCC2017 <https://gcc2017.sciencesconf.org/>* deadlines: 15 April: Oral presentation abstracts <https://gcc2017.sciencesconf.org/page/submit> are due* this Saturday *at 23:59 Paris local time*.* 15 May: Early registration <https://gcc2017.sciencesconf.org/page/registration> ends 27 May: Poster presentation abstracts <https://gcc2017.sciencesconf.org/page/submit> are due. 27 May: Visualization and Computer Demo presentation abstracts <https://gcc2017.sciencesconf.org/page/submit> are due. 31 May: Regular registration <https://gcc2017.sciencesconf.org/page/registration> ends 23 June: Lightning Talk presentation abstracts <https://gcc2017.sciencesconf.org/page/submit> are due. *About GCC2017:* GCC2017 will be in Montpellier, France, 26-30 June and will feature two days of presentations, discussions, poster sessions, lightning talks, computer demos, keynotes, and birds-of-a-feather meetups, all about data-intensive biology and the tools that support it. GCC2017 also includes data and coding hackathons <https://gcc2017.sciencesconf.org/page/hackathon>, and two days of training <https://gcc2017.sched.com/overview/type/Training> covering 16 different topics. GCC2017 will be held at Le Corum Conference Centre <http://www.montpellier-events.com/en/The-Corum/Presentation> in the heart of Montpellier <https://gcc2017.sciencesconf.org/page/location>, just 10km from the Mediterranean. This event will gather several hundred researchers addressing diverse questions and facing common challenges in data intensive life science research. GCC participants work across the tree of life, come from around the world, and work at universities, research organizations, industry, medical schools and research hospitals. If you work in or support data intensive life science research then GCC2017 is an ideal opportunity to present your work. Early registration <https://gcc2017.sciencesconf.org/page/registration> is starts at less than 55€ / day for post-docs and students. You can also book low cost conference housing <https://gcc2017.sciencesconf.org/page/lodging> when you register. GCC2017 has sold out *all* premiere *sponsorship* <https://gcc2017.sciencesconf.org/page/sponsors> slots (a first). If you are interested in sponsoring (or know someone who is) there are still Silver and Bronze and Hackathon sponsorships available. Contact the organisers if you are interested. About Galaxy Galaxy <https://galaxyproject.org/> is an open, web-based platform for data-intensive biomedical analysis used by tens of thousands of researchers around the world. It supports ad hoc exploration and analysis through scalable and repeatable data analysis pipelines for large research studies. Galaxy is available in over 90 free and publicly accessible web servers, on commercial and national cloud infrastructures, and is locally installed at hundreds, if not thousands, of research organisations around the world. We hope to see you this summer in Montpellier! Au revoir, The GCC2017 Organising Committee -- https://galaxyproject.org/ https://getgalaxy.org/ https://usegalaxy.org/ https://gcc2017.sciencesconf.org/

2 1

drmaa on univa grid engine
by Matthias Bernt 13 Apr '17

13 Apr '17

Dear list, I'm struggling to get jobs running on our cluster (UGE). In the galaxy log I see: galaxy.jobs.runners.drmaa DEBUG 2017-04-13 12:24:57,799 (10) submitting file /gpfs1/data/galaxy_server/galaxy-dev/database/jobs_directory/000/10/galaxy_10.sh galaxy.jobs.runners.drmaa DEBUG 2017-04-13 12:24:57,799 (10) native specification is: -l h_rt=60 -l h_vmem=1G -pe smp 2 and I get galaxy.jobs.runners.drmaa WARNING 2017-04-13 12:24:57,805 (10) drmaa.Session.runJob() failed, will retry: code 17: error: no suitable queues But manual submission works: qsub -l h_rt=60 -l h_vmem=1G -pe smp 2 /gpfs1/data/galaxy_server/galaxy-dev/database/jobs_directory/000/10/galaxy_10.sh Your job 161150 ("galaxy_10.sh") has been submitted So I checked if I can use the drmaa library to submit using the following python script (based on the example2 included in the library): """ #!/usr/bin/env python from __future__ import print_function import drmaa import os def main(): """Submit a job. Note, need file called sleeper.sh in current directory. """ s = drmaa.Session() s.initialize() print('Creating job template') jt = s.createJobTemplate() jt.remoteCommand = os.getcwd() + '/sleeper.sh' jt.args = ['42','Simon says:'] jt.joinFiles=True jt.nativeSpecification = "-l h_rt=60 -l h_vmem=1G -pe smp 2" jobid = s.runJob(jt) print('Your job has been submitted with id ' + jobid) print('Cleaning up') s.deleteJobTemplate(jt) s.exit() if __name__=='__main__': main() """ This gives me the same error: drmaa.errors.DeniedByDrmException: code 17: error: no suitable queues So it seems to be a problem related to the drmaa python library. Unfortunately I can not try without any native specs, since time, memory and cores need to be specifies (a suitable queue is chosen automatically). I found an earlier post with the same error (but this seemed to be caused by colons in the file name): http://dev.list.galaxyproject.org/Galaxy-with-Univa-Grid-Engine-UGE-instead… Does anyone has suggestions for me? Best regards, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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