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 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/ >>>>> >>> > ___________________________________________________________ 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/
