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
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