[galaxy-dev] Memory limit for a Travis CI build

[Jin Li]

Hi all,

I submitted a PR to Galaxy Tools IUC
(https://github.com/galaxyproject/tools-iuc/pull/2506). The Travis CI
build exited with an error code 35072. The error may be caused by
running out of memory.
https://travis-ci.org/galaxyproject/tools-iuc/jobs/564531462

In fact, my program does not use too much memory on the test case (<
1GB). May I ask what is the memory limit to pass a Travis CI build?
How could I request more memory if it is too small? Thank you.

Best regards,
Jin
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[galaxy-dev] Re: Installing a database on local instance Galaxy

[Björn Grüning]

Hi,

this will help you hopefully for the blast tools:

https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus#configuration

In short you need to download the UniProt blast DB and edit a file 
called: blastdb_p.loc


Keep in mind Galaxy is framework in which you can run thousands of 
community maintained tools ... it can happen that those tools needs some 
manual work to make them work. This really depends on the tools you have 
installed.


Ciao,
Bjoern

Am 27.07.19 um 10:00 schrieb goutham sarovaram:

Hello,
My name is Goutham I'm currently doing RNA-Seq analysis on a local instance
of Galaxy installed on a workstation at our research center.
As I have been tasked with adminstrative duties for this system I would
like to know how I can install databases on to the local instance
(Databases download from Uniprot and Pfam etc.) For running blast+ and
other tools associated with the trinotate pipeline which I'm trying to
operate through Galaxy.
Best regards.
(The instance is hosted on a Kubuntu 18 LTS with a dual Xeon E series and
64 DDR4 memory, any suggestions for better optimizations are welcome)
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[galaxy-dev] Re: conda not installing deps.

[Jochen Bick]

Hej Björn,

We have activated all conda parameters in the yml. But when you install a tool 
the deps are not installed. So every tool is installed with no deps.

Jochen

⁣Get BlueMail for Android ​

On Jul 26, 2019, 21:07, at 21:07, "Björn Grüning"  
wrote:
>Hi Jochen,
>
>what is not working? Do you have any error message.
>
>Ciao,
>Bjoern
>
>Am 25.07.19 um 15:45 schrieb Jochen Bick:
>> Hi
>> 
>> we have a new galaxy 19.01 instance and conda is somehow not running
>> correctly:
>> 
>> galaxy.yml
>> 
>>    #dependency_resolvers_config_file:
>config/dependency_resolvers_conf.xml
>>    conda_prefix: /opt/galaxy/tools/_conda
>>    #conda_exec: null
>>    #conda_debug: false
>>    #conda_ensure_channels: 'iuc,conda-forge,bioconda,defaults'
>>    #conda_use_local: false
>>    conda_auto_install: true
>>    conda_auto_init: true
>>    conda_copy_dependencies: true
>> 
>>    job_working_directory: /opt/galaxy/daten/jobs_directory
>> 
>> any ideas?
>> 
>> Thanks Jochen
>> 
>> 
>> 
>> 
>> --
>> ETH Zurich
>> *Jochen Bick*
>> Animal Physiology
>> Institute of Agricultural Sciences
>> Postal address: Universitätstrasse 2 / LFW B 58.1
>> 8092 Zurich, Switzerland
>> Office: Eschikon 27
>> 8315 Lindau, Switzerland
>> 
>> Phone +41 52 354 92 06
>> jochen.b...@usys.ethz.ch 
>> www.ap.ethz.ch
>> 
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[galaxy-dev] Installing a database on local instance Galaxy

[goutham sarovaram]

Hello,
My name is Goutham I'm currently doing RNA-Seq analysis on a local instance
of Galaxy installed on a workstation at our research center.
As I have been tasked with adminstrative duties for this system I would
like to know how I can install databases on to the local instance
(Databases download from Uniprot and Pfam etc.) For running blast+ and
other tools associated with the trinotate pipeline which I'm trying to
operate through Galaxy.
Best regards.
(The instance is hosted on a Kubuntu 18 LTS with a dual Xeon E series and
64 DDR4 memory, any suggestions for better optimizations are welcome)
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