date:20180828

Re: [galaxy-dev] java options

2018-08-28 Thread Matthias Bernt


Hi Bjoern,


So, it seems that the best option is to:
- switching back to _JAVA_OPTIONS (which seems to be implemented also 
on usegalaxy.org)

- handling the output in each java tool


This is also what usegalaxy.eu is using and we have special destinations 
for java tools.


Indeed, this seems to be the best option.



Are there any guidelines for wrapping java based applications (or 
other programming languages)?


- add java to dependencies? I think this should be done, or?


This should be part of the dependencies of your tool already, isn't it?
So MSGFplus should depend on a java version of their choice.

See here: 
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/msgf_plus/meta.yaml#L15 


I still tend to forget that conda also has dependencies .. of course 
this makes more sense than having a galaxy dependency.



- if yes: is there a favored conda package?


openjdk if needed.


OK. Thanks also to you.

Best,
Matthias




Ciao,
Bjoern


Cheers,
Matthias

P.S. I just added java to my list of despicable programming languages.

On 27.08.2018 12:00, Marius van den Beek wrote:

Hi Matthias,

if a tool prints something to the stderr that is indeed considered to 
indicate a failure, and it's the default mostly because
we don't want to break legacy tools that make this assumption. If you 
include a profile version in your tool
or change your command section to detect_errors="exit_code"> this will more reasonably 
determine

if a tool failed based on the exit code.

Best,
Marius

On Mon, 27 Aug 2018 at 11:52, Matthias Bernt > wrote:


    Dear list,

    I'm struggling to set java options for galaxy tools. Currently I use
    ` in my job_conf.xml and in the 
script

    I explored two ways to set java options:

    `_JAVA_OPTIONS="-Xmx5G -Xms1G -Djava.io.tmpdir=/work/songalax/tmp"`

    But then java prints "Picked up _JAVA_OPTIONS: ..." to stderr 
which is
    be interpreted as error by some tools. If I'm correct this is 
currently
    the default .. I have seen this happening, but can't remember the 
name

    of the tool.

    So I switched to this 'trick':

    `alias java='java -Xmx5G -Xms1G 
-Djava.io.tmpdir=/work/songalax/tmp'`


    but the problem is that the tool script is called and not sourced 
and
    therefore aliases are not used (could this be changed?). 
Furthermore,

    for tools which explicitly set the java options my settings would be
    ignored anyway (an example is the MSGFPlusAdapter which calles `java
    -Xmx3500m` .. so my -Xmx is overwritten .. I passing
    GALAXY_MEMORY_MB to
    the corresponding parameter might be a solution for this tool).

    Any thought or suggestions on how to set the parameters in a 
production

    environment are very welcome.

    Cheers,
    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.be...@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
    ---
    ___
    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/

    To search Galaxy mailing lists use the unified search at:
    http://galaxyproject.org/search/





--

---
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.be...@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
---
___
Please keep all

Re: [galaxy-dev] java options

2018-08-28 Thread Björn Grüning

Hi Matthias,

Hi Marius,

Thanks for your comments. That's what I thought.

> To me this sounds like something that really should be fixed in the
> tool as presumably this affects every deployer.

Hmm. The 'tool' would be java. As far as I have seen java is
never/seldom in the tool dependencies. Hence, the system's java
installation is used for which we do not know if it is Sun/OpenJDK or
which version it is (in addition the installation will likely not change
on production systems for a long time). So I guess fixing this in java
would not help here in reasonable time anyway.

So, it seems that the best option is to:
- switching back to _JAVA_OPTIONS (which seems to be implemented also on
usegalaxy.org)

- handling the output in each java tool

This is also what usegalaxy.eu is using and we have special destinations
for java tools.

Are there any guidelines for wrapping java based applications (or other
programming languages)?

- add java to dependencies? I think this should be done, or?

This should be part of the dependencies of your tool already, isn't it?
So MSGFplus should depend on a java version of their choice.

See here:
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/msgf_plus/meta.yaml#L15

- if yes: is there a favored conda package?

openjdk if needed.

Ciao,
Bjoern

Cheers,
Matthias

P.S. I just added java to my list of despicable programming languages.

On 27.08.2018 12:00, Marius van den Beek wrote:

Hi Matthias,

if a tool prints something to the stderr that is indeed considered to
indicate a failure, and it's the default mostly because
we don't want to break legacy tools that make this assumption. If you
include a profile version in your tool
or change your command section to detect_errors="exit_code"> this will more reasonably determine

if a tool failed based on the exit code.

Best,
Marius

On Mon, 27 Aug 2018 at 11:52, Matthias Bernt > wrote:

Dear list,

I'm struggling to set java options for galaxy tools. Currently I use
` in my job_conf.xml and in the
script

I explored two ways to set java options:

`_JAVA_OPTIONS="-Xmx5G -Xms1G -Djava.io.tmpdir=/work/songalax/tmp"`

But then java prints "Picked up _JAVA_OPTIONS: ..." to stderr
which is
be interpreted as error by some tools. If I'm correct this is
currently
the default .. I have seen this happening, but can't remember the
name

of the tool.

So I switched to this 'trick':

`alias java='java -Xmx5G -Xms1G -Djava.io.tmpdir=/work/songalax/tmp'`

but the problem is that the tool script is called and not sourced and
therefore aliases are not used (could this be changed?). Furthermore,
for tools which explicitly set the java options my settings would be
ignored anyway (an example is the MSGFPlusAdapter which calles `java
-Xmx3500m` .. so my -Xmx is overwritten .. I passing
GALAXY_MEMORY_MB to
the corresponding parameter might be a solution for this tool).

Any thought or suggestions on how to set the parameters in a
production

environment are very welcome.

Cheers,
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.be...@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
---
___
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/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/

___
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/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/

Re: [galaxy-dev] java options

Re: [galaxy-dev] java options

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