[galaxy-dev] galaxy venv problem

2016-10-28 Thread Beginner TI 
Hi,

During the installation or galaxy instance, I set up a directory to install
all the python dependencies. Basically, whenever I install python modules,
I do something like:

python setup.py install --prefix=/my/python/dir

as a result, there are tons of stuff installed there. I added this path to
PYTHONPATH.

The reason I do this is that I don't want to use sudo to install galaxy
python modules.

Now the problem...I was hoping not to use virtual env.  However galaxy is
set to use it's own venv, and during the course of starting, it will unset
the PYTHONPATH. That caused that installed tools didn't work because it
could not find the modules installed.

Here is one example of how it is not working. The tool generated the
following command in the script:

gca -b
/media/libraryfiles/galaxy-data-store/database/files/000/dataset_44.dat
--span=3000 -g
/media/libraryfiles/dep/cistrome-static-lib/ceaslib/GeneTable/mm9
--name=gca_out >&
/media/libraryfiles/galaxy-data-store/database/files/000/dataset_95.dat
cp gca_out.xls
/media/libraryfiles/galaxy-data-store/database/files/000/dataset_94.dat

I could run that command in the terminal successfully, but not in the
galaxy. It keeps reporting error that gca_out.xls isn't there. With the
PYTHONPATH unset, when I run that command, I would get:

Traceback (most recent call last):
  File "/media/libraryfiles/dep/python/bin/gca", line 32, in 
import CEAS.inout as inout
ImportError: No module named CEAS.inout

Once I put the PYTHONPATH back,

export PYTHONPATH=/media/libraryfiles/dep/python/lib/python2.7/site-packages

then that gca command would generate the correct output file.

I tried to use

sh run.sh --skip-venv

However, it keeps giving me errors. It seems those were from not able to
install the dependencies listed in requirements.txt.

I then installed those dependencies to my python directory as well. During
the course had to remove some that came with system, and install the newer
ones.

Now it seems to be working. I'm just wondering, is this a good way to using
system python with all the dependencies I installed?

Thanks,
Rui
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[galaxy-dev] Call for GMOD talks at PAG

2016-10-28 Thread Scott Cain 
Hi,

I am pleased to announce a call for talks to be given at the Plant and
Animal Genomes conference this January in the GMOD workshop on Wednesday,
January 18th.  Any talks that involve the development or use of GMOD
software are welcome.  In particular this year, I'd really like to
highlight plugins for the various GMOD software packages that support them,
like JBrowse, Galaxy and Tripal (of course, Galaxy and Tripal have their
own sessions, so you should consider submitting to them too).

Please get an abstract, brief summary or a vague title to me as soon as
possible so I can start getting it put together.  Also, if you'd like to be
a co-organizer, please let me drop me a line about that too.  I might be
able to get you some meeting-related niceties for not very much work.

For more information about PAG, see:

  http://www.intlpag.org

Thanks and I look forward to seeing in January,
Scott


-- 

Scott Cain, Ph. D.   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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Re: [galaxy-dev] odose

2016-10-28 Thread Björn Grüning 
Hi Michiel,

the IUC (https://github.com/galaxyproject/tools-iuc) is adopting
wrappers and helping with fixing them. Can you create a PR with
everything what you have against this repo, we will review it and guide
you through the process. Once, this is merged we will help maintaining it.

Thanks,
Bjoern

Am 25.10.2016 um 13:54 schrieb Vos, Michiel:
>  
> 
> Dear Galaxy developers,
> 
>  
> 
> We hereby want to ask if anyone is interested in helping out to repair
> and update our Galaxy tool ‘odose’:
> 
>  
> 
> Webserver 
> 
>  
> 
> Publication
> 
> 
>  
> 
> Public server page
> 
> 
>  
> 
> Github 
> 
>  
> 
> Odose enables users to perform an array of population genetics tests on
> prokaryote genomes. Our tool is currently linked to NCBI to download
> various files, but continuous restructuring at NCBI has resulted in
> broken links which prevent the pipeline from working. Developer Tim te
> Beek has moved on outside academia and does not have the time to fix it,
> but is available to give answer question/give instructions. We believe
> our tool is highly useful for microbiologists and would greatly
> appreciate any help from the Galaxy community to get it working properly
> again! Please get in touch if you would like to know more.
> 
>  
> 
> Best Wishes, Michiel Vos, Mark van Passel and Tim te Beek
> 
>  
> 
>  
> 
>  
> 
> Michiel Vos
> 
> European Centre for Environment and Human Health
> 
> University of Exeter
> 
> ESI Building, Penryn Campus
> 
> TR10 9FE Penryn, UK
> 
> 0044 (0)1326259464
> 
> https://coastalpathogens.wordpress.com/
> 
>  
> 
> 
> 
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Re: [galaxy-dev] conda management of tools dependent on python3

2016-10-28 Thread Björn Grüning 
Hi Wolfgang,

can you describe step by step what you are trying to do?

A conda package ships it's own python version, you can see this in the
build-string py35_0 for example. So conda can handle all python version
independent of the python version of miniconda.

Cheers,
Bjoern

> Dear all,
> 
> I'm still pretty new to conda tool dependencies management and there is
> one thing I cannot find documented anywhere:
> How can I let conda manage tool dependencies that involve python3?
> If I let Galaxy install conda for me, it creates an environment with
> python2, then if there is a tool dependency that has a conda package
> built for only python3 I'm getting an error because of a conflict
> between that package and python2 (not surprisingly), but AFAIU conda
> environments are bound to one particular version of python (or is that
> incorrect?).
> 
> Thanks for any help with this and best wishes,
> Wolfgang
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[galaxy-dev] Usegalaxy.org Data Rsync Connection refused

2016-10-28 Thread Georgios Nikolis 

  
  
Dear all,
we are currently working on setting up a new local Galaxy
installation and I would like to obtain the genome reference data
available on the public Galaxy instance. I am following the
instructions on the Wiki page
(https://wiki.galaxyproject.org/Admin/UseGalaxyRsync), but I can't
seem to be able to access datacache.g2.bx.psu.edu via rsync. 
rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX .
rsync: failed to connect to datacache.g2.bx.psu.edu
(128.118.250.10): Connection refused (111)
rsync error: error in socket IO (code 10) at clientserver.c(128)
[Receiver=3.1.1]

Does anyone know if the URL has changed in the meantime? Is there
any alternative way to access this data?

Thanks in advance!

Best regards,
Georgios


-- 
  Georgios
  Nikolis
Genomics and Proteomics
Core Facility
High Throughput Sequencing (W190)
IT Management Genomics Proteomics

  
  German Cancer Research Center (DKFZ)
  Foundation under Public Law
  Im Neuenheimer Feld 580
  69120 Heidelberg
  Germany
  phone: +49 6221 42-4659

  g.niko...@dkfz.de
  www.dkfz.de

  
  

  Management
  Board: Prof. Dr. Michael Boutros (interim), Prof. Dr. Josef
  Puchta
  VAT-ID No.: DE143293537
  

   
  
  


  



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