fonts on headless compute nodes

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

fonts on headless compute nodes

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




--

-------------------------------------------
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,
[hidden email], 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
-------------------------------------------
___________________________________________________________
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/
Reply | Threaded
Open this post in threaded view
|

Re: fonts on headless compute nodes

Björn Grüning-3
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
>
>
>
>
___________________________________________________________
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/