Hi Nicola,
thanks. That worked.
Matthias
On 25.04.2018 12:07, Nicola Soranzo wrote:
Hi Matthias,
if you add
'openjdk >8.0.121'
to your conda command below, you should get openjdk from conda-forge.
For an explanation, see:
https://github.com/bioconda/bioconda-recipes/pull/8588
https://github.com/conda/conda/issues/6948#issuecomment-369360906
Cheers,
Nicola
On 25/04/18 10:44, Matthias Bernt wrote:
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 bioconda
--channel conda-forge --channel defaults --name __fastqc@0.11.5
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
--
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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,
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