Re: [galaxy-dev] OpenBabel Requirements
Hi Matthias, so I spend a few hours to upgrade most (not all) tools to conda. This was overdue ... I also put togehter a Docker container: https://github.com/bgruening/docker-galaxy-chemicaltoolbox You can start it with: docker run -i -t -p 8080:80 quay.io/bgruening/galaxy-chemicaltoolbox Tools included in this container should work everywhere. I found 1 small bug already and will fix this in the next week, but it should work most of the times :) Which tools had the blat dependency? As long as you deal with package_* repositories you are not using conda packages and then you need to have these cmake, gcc dependencies isntalled. Cheers, Bjoern Am 19.05.2017 um 13:45 schrieb Matthias Bernt: > Hi Bjoern, > > I thought I'm using conda .. :). I'm using the ansible > galaxy-tools-playbook to install tools. I tried before if ansible > installation and installation via the web interface give the same > results -- and I recalled that the results were identical. But I was > wrong -- sorry for the inconvenience. > > Now, when installing via ansible I'm getting identical (compared to > installation via the web interface) results for blat I choose the > following options in the tool_list.yaml file. > install_tool_dependencies: False > install_repository_dependencies: True > install_resolver_dependencies: True > > But I still have not understood the dependencies (and dependency > problems) shown in the web interface... Maybe you could explain this to me? > > In the logs there is first a complaint about missing > - blat 35x1* > then the following packages are installed: > blat: 35-1 bioconda > libpng: 1.6.27-0 > zlib: 1.2.8-3 > > The admin interface puzzles me: For the blat package: > - "Dependency Resolver Details" lists blat 35x1 as resolved but not the > exact version. This seems to be fine. > - Installed repository dependencies lists package_blat_35x1 as installed > but missing dependencies. This is odd? Why is this installed at all? > > For the package_blat_35x1 > - Installed repository dependencies lists package_libpng_1_6_7 > - Missing tool dependencies lists blat and libpng. The circular > dependency to blat is strange, isn't it? > > Thanks again for the support. > > Cheers, > Matthias > > On 18.05.2017 17:09, Björn Grüning wrote: >> Hi Matthias, >> >> is there any chance you can upgrade your Galaxy and enable conda >> packages? >> This would make your life so much easier :) >> >> Cheers, >> Bjoern >> >> Am 18.05.2017 um 16:28 schrieb Matthias Bernt: >>> Hi Bjoern, >>> >>> thanks for the explanation. This helped for the openbabel package. Still >>> there are some packages where I have problems. I guess this is because >>> on our system the libraries are mostly at non-default locations. >>> >>> Currently I have problems to install BLAT. It complains about a missing >>> zlib. Zlib is installed and the path to the includes is in CPPFLAGS. Is >>> there any variable that would make it known to the installation process? >>> >>> gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized >>> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOU >>> RCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DCOLOR32 -Wall -Wformat >>> -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc >>> -I../../../inc -I../../../../inc -I../../../../../inc >>> -I/gpfs1/data/galaxy_server/gala >>> xy-dev/database/dependencies/libpng/1.6.7/devteam/package_libpng_1_6_7/3de32cd300a9/include >>> >>> -o zlibFace.o -c zlibFace.c >>> make: Leaving directory >>> `/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtd4Jyr2N/blat/src >>> >>> >>> /lib' >>> zlibFace.c:4:18: error: zlib.h: No such file or directory >>> >>> An additional question for understanding: There are packages for zlib >>> and cmake (as example). Why are these not used? Is this because there is >>> still transition to conda -- which will just need time? But from an >>> earlier post I thought I understood that package_* is the old non-conda >>> way. >>> Or is the intended future state that central packages mentioned in >>> https://galaxyproject.org/toolshed/package-recipes/ >>> are managed on the system .. and not conda? >>> >>> Thanks a lot. >>> >>> Cheers, >>> Matthias >>> >>> >>> >>> On 17.05.2017 20:08, Björn Grüning wrote: Hi Matthias, if you are installing repositories that still rely on the old traditional Galaxy system you need to have a few packages installed locally, see this list: https://galaxyproject.org/toolshed/package-recipes/ However, we have now a new dependency system in Galaxy, that is build on-top of conda and most of the Cheminformatic tools have been ported to Conda already. Which version of Galaxy are you running? But maybe I have also not pushed the latest changes to the toolshed which I have been working on github :( Ciao, Bjoern Am 17.05.2017 um 17:04 schrieb Matthias Bernt: > Dear galaxy-dev
Re: [galaxy-dev] OpenBabel Requirements
Hi Bjoern, I thought I'm using conda .. :). I'm using the ansible galaxy-tools-playbook to install tools. I tried before if ansible installation and installation via the web interface give the same results -- and I recalled that the results were identical. But I was wrong -- sorry for the inconvenience. Now, when installing via ansible I'm getting identical (compared to installation via the web interface) results for blat I choose the following options in the tool_list.yaml file. install_tool_dependencies: False install_repository_dependencies: True install_resolver_dependencies: True But I still have not understood the dependencies (and dependency problems) shown in the web interface... Maybe you could explain this to me? In the logs there is first a complaint about missing - blat 35x1* then the following packages are installed: blat: 35-1 bioconda libpng: 1.6.27-0 zlib: 1.2.8-3 The admin interface puzzles me: For the blat package: - "Dependency Resolver Details" lists blat 35x1 as resolved but not the exact version. This seems to be fine. - Installed repository dependencies lists package_blat_35x1 as installed but missing dependencies. This is odd? Why is this installed at all? For the package_blat_35x1 - Installed repository dependencies lists package_libpng_1_6_7 - Missing tool dependencies lists blat and libpng. The circular dependency to blat is strange, isn't it? Thanks again for the support. Cheers, Matthias On 18.05.2017 17:09, Björn Grüning wrote: Hi Matthias, is there any chance you can upgrade your Galaxy and enable conda packages? This would make your life so much easier :) Cheers, Bjoern Am 18.05.2017 um 16:28 schrieb Matthias Bernt: Hi Bjoern, thanks for the explanation. This helped for the openbabel package. Still there are some packages where I have problems. I guess this is because on our system the libraries are mostly at non-default locations. Currently I have problems to install BLAT. It complains about a missing zlib. Zlib is installed and the path to the includes is in CPPFLAGS. Is there any variable that would make it known to the installation process? gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOU RCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I/gpfs1/data/galaxy_server/gala xy-dev/database/dependencies/libpng/1.6.7/devteam/package_libpng_1_6_7/3de32cd300a9/include -o zlibFace.o -c zlibFace.c make: Leaving directory `/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtd4Jyr2N/blat/src /lib' zlibFace.c:4:18: error: zlib.h: No such file or directory An additional question for understanding: There are packages for zlib and cmake (as example). Why are these not used? Is this because there is still transition to conda -- which will just need time? But from an earlier post I thought I understood that package_* is the old non-conda way. Or is the intended future state that central packages mentioned in https://galaxyproject.org/toolshed/package-recipes/ are managed on the system .. and not conda? Thanks a lot. Cheers, Matthias On 17.05.2017 20:08, Björn Grüning wrote: Hi Matthias, if you are installing repositories that still rely on the old traditional Galaxy system you need to have a few packages installed locally, see this list: https://galaxyproject.org/toolshed/package-recipes/ However, we have now a new dependency system in Galaxy, that is build on-top of conda and most of the Cheminformatic tools have been ported to Conda already. Which version of Galaxy are you running? But maybe I have also not pushed the latest changes to the toolshed which I have been working on github :( Ciao, Bjoern Am 17.05.2017 um 17:04 schrieb Matthias Bernt: Dear galaxy-dev list, I have problems to install package_openbabel. The problem seems to be that cmake is not found during installation. The documentation also states that: "Compiling OpenBabel requires g++ and CMake 2.4+" My question is: Does this refer to cmake installed on the system or in galaxy (since there is also package_cmake_3_2_3)? Thanks a lot. Cheers, Matthias ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ -- --- 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.be...@ufz.de, www.ufz.de Sitz der
Re: [galaxy-dev] OpenBabel Requirements
Hi Bjoern, thanks for the explanation. This helped for the openbabel package. Still there are some packages where I have problems. I guess this is because on our system the libraries are mostly at non-default locations. Currently I have problems to install BLAT. It complains about a missing zlib. Zlib is installed and the path to the includes is in CPPFLAGS. Is there any variable that would make it known to the installation process? gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOU RCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I/gpfs1/data/galaxy_server/gala xy-dev/database/dependencies/libpng/1.6.7/devteam/package_libpng_1_6_7/3de32cd300a9/include -o zlibFace.o -c zlibFace.c make: Leaving directory `/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtd4Jyr2N/blat/src /lib' zlibFace.c:4:18: error: zlib.h: No such file or directory An additional question for understanding: There are packages for zlib and cmake (as example). Why are these not used? Is this because there is still transition to conda -- which will just need time? But from an earlier post I thought I understood that package_* is the old non-conda way. Or is the intended future state that central packages mentioned in https://galaxyproject.org/toolshed/package-recipes/ are managed on the system .. and not conda? Thanks a lot. Cheers, Matthias On 17.05.2017 20:08, Björn Grüning wrote: Hi Matthias, if you are installing repositories that still rely on the old traditional Galaxy system you need to have a few packages installed locally, see this list: https://galaxyproject.org/toolshed/package-recipes/ However, we have now a new dependency system in Galaxy, that is build on-top of conda and most of the Cheminformatic tools have been ported to Conda already. Which version of Galaxy are you running? But maybe I have also not pushed the latest changes to the toolshed which I have been working on github :( Ciao, Bjoern Am 17.05.2017 um 17:04 schrieb Matthias Bernt: Dear galaxy-dev list, I have problems to install package_openbabel. The problem seems to be that cmake is not found during installation. The documentation also states that: "Compiling OpenBabel requires g++ and CMake 2.4+" My question is: Does this refer to cmake installed on the system or in galaxy (since there is also package_cmake_3_2_3)? Thanks a lot. Cheers, Matthias ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ -- --- 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.be...@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 --- smime.p7s Description: S/MIME Cryptographic Signature ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
