Hi Bjoern,
still struggling with your suggestion:
> can you make sure FASTQC gets the openjdk version from conda-forge and
> not from defaults? This will fix our one problem.
conda create -y --override-channels --channel iuc --channel bio
conda --channel conda-forge --channel defaults --name [email protected]
fastqc=0.11.5
fastqc: 0.11.5-pl5.22.0_3 bioconda
openjdk: 8.0.121-1
perl: 5.22.0.1-0 conda-forge
removing --channel defaults still resulted in the same.
Then I upgraded conda (4.3.27-py35h1706b01_0 --> 4.5.1-py35_0), and now
at least removing the defaults channel has an effect .. but still
openjdk is not installed from conda-forge (instead an ominous zulu jdk
is installed from bioconda):
fastqc: 0.11.5-1 bioconda
java-jdk: 8.0.92-1 bioconda
Any comments on this?
Best,
Matthias
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
--
-------------------------------------------
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,
[email protected], 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/
