[galaxy-dev] updated eggs needed for OS X El Capitan compatibility

[Wolfgang Maier]

Hi,

today, there was a complaint on the Galaxy Biostar forum that Galaxy 
fails to start under the new OS X El Capitan 
(https://biostar.usegalaxy.org/p/14492/).


I had noticed this last week already, and that post prompted me to 
investigate the problem in more detail.
The result (now checked on our own Galaxy instance) is that 
compatibility with El Capitan requires updates to two eggs - amqp and 
kombu - in the sense that, at least, you can start Galaxy after fixing 
these two. I haven't checked to see if there are additional run time 
problems.


Hope that information helps,
Wolfgang

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Re: [galaxy-dev] Workflow 'Input Dataset' Ressolution Issue

[John Chilton]

No if you update to the latest release_15.07 it should be fixed. I
don't know if CloudMan has an easy way to do that, but you can do it
from the command-line with something like the following commands:

% git fetch --all
% git checkout release_15.07

-John

On Mon, Oct 12, 2015 at 4:09 AM, Marco Albuquerque
 wrote:
> So in other words, there is no release that I can update my cloudman
> instance to?
>
> Marco
>
> On Sun, Oct 11, 2015 at 3:49 PM, John Chilton  wrote:
>>
>> Yeah - release_15.07 is a moving target that bug fixes get added to.
>> 990501d2d9 doesn't seem to have this fix yet.
>>
>> On Sun, Oct 11, 2015 at 5:09 PM, Marco Albuquerque
>>  wrote:
>> > Well, my Cloudman galaxy instance is installing 15.07 revision
>> > 990501d2d9.
>> >
>> > Is there maybe a different revision I should be using?
>> >
>> > Marco
>> >
>> > On Sun, Oct 11, 2015 at 11:03 AM, John Chilton 
>> > wrote:
>> >>
>> >> This sounds like it corresponds to this issue
>> >> https://github.com/galaxyproject/galaxy/issues/776. Is it possible
>> >> that upgrading Galaxy to the latest 15.07 fixes the issue?
>> >>
>> >> On Thu, Oct 8, 2015 at 7:40 PM, Marco Albuquerque
>> >>  wrote:
>> >> > Hello Galaxy Dev,
>> >> >
>> >> > Consider the workflow found in 'Strelka_Workflow_Sequential' image
>> >> >
>> >> > Here it is in a different view
>> >> > 'Strelka_Sequential_Workflow_Different_View'
>> >> >
>> >> > Notice That the first input dataset links to the fetch_interval tool
>> >> > and
>> >> > the
>> >> > first preprocess tool. And the second input dataset links only to the
>> >> > second
>> >> > preprocess tool.
>> >> >
>> >> > When you run the workflow, what actually happens is the first input
>> >> > dataset
>> >> > goes to the fetch_interval tools and the second input dataset goes to
>> >> > both
>> >> > preprocessing tools. (Look at final two images). They have
>> >> > essentially
>> >> > executed the same tool twice. Where it should be an execution with a
>> >> > normal
>> >> > file and an execution with a tumour file.
>> >> >
>> >> > Why is this happening? What can I do to fix this?
>> >> >
>> >> > Thanks,
>> >> >
>> >> > Marco Albuquerque
>> >> >
>> >> > ___
>> >> > 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:
>> >> >   http://galaxyproject.org/search/mailinglists/
>> >
>> >
>
>
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Re: [galaxy-dev] Get the working directory within the ncbi_blastp_wrapper.xml file

[John Chilton]

I'd keep working on pbs_python or switch to drmaa that frequently
works for the same distribution. There is also a CLI runner that just
executes qsub and qstat commands directly on the localhost or can also
ssh into a remote host and execute these commands.

https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L22
https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L399

If you must modify the wrapper to add a qsub in there - can you grab
the working directory at runtime? I don't think it is actually exposed
at command generation time.

CWD=`pwd`; qsub ... $CWD

Something like that, I don't know.

-John





On Tue, Sep 15, 2015 at 11:08 PM, Ryan Johnson  wrote:
> Hello all,
>
> We are setting up a galaxy instance that will submit jobs to our cluster. We
> could not get pbs_python to work so we have added all PBS logic to the
> cheetah template wrapper ncbi_blastp_wrapper.xml.
>
> Currently, all jobs are running out of the home directory. We want to add
> logic to the wrapper which will get the working directory from the
> JobWrapper class and then change to that directory and run from there.
>
> Can anyone help us to access the JobWrapper.working_underscore value? Or
> suggest a better way to do this?
>
> Thank you very much,
>
> Ryan
>
>
> --
> Ryan S. Johnson, PhD
>   Applications Scientist
>   Center for Advanced Research Computing
>   P: (650) 430-6194
>   E: rjohn...@carc.unm.edu
>
>
>
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Re: [galaxy-dev] GCC2016 Training Day Topic Nominations are now open

[Dave Clements]

Hello all,

Just a final reminder that GCC2016 Training Topics are determined by you,
the Galaxy Community, and that Training Topic Nomination *closes this
Friday*.  So far we have 8 nominated topics:
  bit.ly/gcc2016trn

If you don't see the topics you want offered, then please nominate those
topics this week.
  http://bit.ly/gcc2016tdnom

Thanks, and hope to see you at GCC2016!

Dave C



On Mon, Sep 28, 2015 at 11:34 AM, Dave Clements 
wrote:

> Hello all,
>
> The 2016 Galaxy Community Conference (GCC2016)
>  features two full days of
> training on June 26-27. Each day will have multiple tracks, with each
> track featuring several sessions throughout the day. GCC2016 will be held
> at Indiana University  in Bloomington, Indiana,
> United States.
>
> *GCC2016 Training topics
>  are nominated by
> you , the Galaxy Community.* Please give some
> thought to what topics you would like to see offered, or that you would
> like to offer, and then submit them as topic nominations
> . Any topic of interest to the Galaxy
> Community can be nominated and you are encouraged to nominate more than one
> topic. If you are looking for ideas, see
>
>-
>
>Topics nominated for GCC2015 
>-
>
>Topics nominated for GCC2014 
>-
>
>Topics nominated for GCC2013 
>-
>
>The Galaxy Events page , which
>lists what training the community is offering outside of GCCs.
>-
>
>Topics that have already been nominated for GCC2016
>
>
> *Please nominate a topic now!  *
>
> Nominated topics will be published as they come in
> 
> . *Topic nomination closes Friday, October, 16.*. Topics will be compiled
> into a uniform list by the GCC2016 Organizing Committee, and topics will be
> voted on by the Galaxy Community from October 26 through November 6.
>
> Topics will then be selected and scheduled based on topic interest, and
> the organisers' ability to confirm instructors for each session.  Some very
> popular sessions may be scheduled more than once. The final schedule will
> be posted before registration opens.
>
> Looking forward to a stellar set of nominations, and hoping to see you in
> Bloomington,
>
> GCC2016 Exec Committee
> 
> --
> http://galaxyproject.org/
> http://getgalaxy.org/
> http://usegalaxy.org/
> https://wiki.galaxyproject.org/
>



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Re: [galaxy-dev] updated eggs needed for OS X El Capitan compatibility

[Dannon Baker]

Hi Wolfgang,

Thanks for the extensive testing!  I hadn't noticed this since I was using
a brew-installed python in a virtualenv, but I can confirm that this is
broken with the new OSX system python.  I'll build and test a few updated
eggs now.

-Dannon

On Mon, Oct 12, 2015 at 6:18 AM Wolfgang Maier <
wolfgang.ma...@biologie.uni-freiburg.de> wrote:

> Hi,
>
> today, there was a complaint on the Galaxy Biostar forum that Galaxy
> fails to start under the new OS X El Capitan
> (https://biostar.usegalaxy.org/p/14492/).
>
> I had noticed this last week already, and that post prompted me to
> investigate the problem in more detail.
> The result (now checked on our own Galaxy instance) is that
> compatibility with El Capitan requires updates to two eggs - amqp and
> kombu - in the sense that, at least, you can start Galaxy after fixing
> these two. I haven't checked to see if there are additional run time
> problems.
>
> Hope that information helps,
> Wolfgang
>
> ___
> 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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>   http://galaxyproject.org/search/mailinglists/
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