if you add
to your conda command below, you should get openjdk from conda-forge.
For an explanation, see:
On 25/04/18 10:44, Matthias Bernt wrote:
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(a)0.11.5
fastqc: 0.11.5-pl5.22.0_3 bioconda
perl: 126.96.36.199-0 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?
> 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:
>> 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.