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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