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/
