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
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-- ------------------------------------------- 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@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 -------------------------------------------