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