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, m.bernt@ufz.de, 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 -------------------------------------------
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
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 __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
-- ------------------------------------------- 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, m.bernt@ufz.de, 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 -------------------------------------------
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
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
-- ------------------------------------------- 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, m.bernt@ufz.de, 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 -------------------------------------------
participants (3)
-
Björn Grüning -
Matthias Bernt -
Nicola Soranzo