Hi Matthias, can you make sure FASTQC gets the openjdk version from conda-forge and not from defaults? This will fix our one problem. MetaProSIP should add additional dependencies to the conda package. Ideally no requirements are needed on the system level. This is not always possible, for example for opengl dependent stuff, but we should try to fix the conda package as much as possible as this will give us also robust containers. Cheers, Bjoern Am 11.04.2018 um 14:51 schrieb Matthias Bernt:
Dear list,
I found that some tools (eg FastQC and MetaProSIP) have problems with missing fonts (the former is java and the latter caused by R) on our compute nodes which do not have xorg and no fonts installed.
On the cluster head nodes several font related packages are installed:
dejavu-fonts-common-2.33-1.el6.noarch xorg-x11-fonts-Type1-7.2-11.el6.noarch liberation-fonts-common-1.05.1.20090721-5.el6.noarch liberation-sans-fonts-1.05.1.20090721-5.el6.noarch dejavu-sans-fonts-2.33-1.el6.noarch urw-fonts-2.4-11.el6.noarch ghostscript-fonts-5.50-23.2.el6.noarch xorg-x11-fonts-misc-7.2-11.el6.noarch
It seems that conda no fonts are available. Is there somebody with similar problems. Any hint which of the packages is/are actually needed. Maybe our admins could install them...
I also found for MetaProSIP that several xorg-... packages are needed. Should such dependencies be handled by the conda packages or by the Galaxy tool.
Best, Matthias