fonts on headless compute nodes

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fonts on headless compute nodes

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,
[hidden email], 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
-------------------------------------------
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Re: fonts on headless compute nodes

Björn Grüning-3
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
>
>
>
>
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Re: fonts on headless compute nodes

Matthias Bernt
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,
[hidden email], 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/

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Re: fonts on headless compute nodes

Nicola Soranzo-2
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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in your mail client.  To manage your subscriptions to this
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Re: fonts on headless compute nodes

Matthias Bernt
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,
[hidden email], 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:
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To search Galaxy mailing lists use the unified search at:
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