Re: [galaxy-user] Galaxy logo: licence? (blog article project)

2012-04-11 Thread Louise-Amélie Schmitt 

Hello Jen,

That helped a lot, thank you! I didn't know the license also applied to 
the images.


Best,
L-A

Le 11/04/2012 15:45, Jennifer Jackson a écrit :

Hello L-A,

Galaxy is open-source for all components, the license is here:
http://bitbucket.org/galaxy/galaxy-central/src/3f12abbd2394/LICENSE.txt

And in case you haven't seen this wiki, section 3 lists some preferred 
link URLs:

http://wiki.g2.bx.psu.edu/Citing%20Galaxy

We'll send more comments as the team has a chance to discuss. Please 
let us know if we can help with anything else.


Thanks!

Jen
Galaxy team

On 4/11/12 2:10 AM, Louise-Amélie Schmitt wrote:

Hello,

I want to write an article on Galaxy on our bioinformatics blog (
http://bioinfo-fr.net/), so I would like to know what materials I can
use and under which conditions. What is the licence of the pictures
(logo etc.)? Can I use them?

Is there anything particular you want me to mention?

Thanks,
L-A


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Re: [galaxy-user] BAM files loading and mandatory grooming

2011-07-19 Thread Louise-Amélie Schmitt 

Hello Jennifer, and thanks for your answer



Would you be able to help with a bit more detail and testing? #2 
sounds like it may be the issue, but without knowing more right now, 
I'll provided the next troubleshooting steps.


Yeah, I realise I was not very clear, sorry about that.



1 - this is in your own install and it is current with the latest 
-dist or are you using -central (which pull?). Did something change 
between the last successful BAM load and the new problem?


This is indeed a local install (two of them actually).
$ hg head
changeset:   5585:8c11dd28a3cf
tag: tip
user:Nate Coraor n...@bx.psu.edu
date:Thu May 19 10:07:53 2011 -0400
summary: Add Picard and fastqc tools to Main

I can't remember whether I ever could successfully load a bam file...



2 - without copying them means maybe that you are using a symbolic 
link at your own site? This load is into a Library (this is how to 
move data transferred outside of the Galaxy mechanisms into a history, 
i.e. around a local file system by direct copy or similar). Load into 
a Library first, then copy to history. Instruction in wiki here:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files 



No, it's just that when I add new datasets to a library from filesystem 
paths I choose the 'Link files without copying into Galaxy' option.




3 - or do you mean without copying by using the FTP method set up 
locally, followed by a load into a history?


4 - BAM file metadata (pencil icon - Edit options) looks OK? Or, this 
is the problem?


It looks ok. Well I guess. When I click on the file in the library, in 
the 'Miscellaneous information' section I have:
The uploaded files need grooming, so change your Copy data into Galaxy? 
selection to be Copy files into Galaxy instead of Link to files without 
copying into Galaxy so grooming can be performed.




5 - SAMTools is loaded into your instance? Tools function on other BAM 
files or all? Some simple SAMTools commands (that work with BAM files) 
function line command OK on these (to rule out problem with BAM files 
themselves - missing .bai index could be a problem).


Samtools works like charm. I've been using it through these Galaxy 
instances for a long time now.




6 - if you start with the same data and convert SAM-BAM within 
Galaxy, does the SAM load and is the resulting BAM file OK?


I can't run anything on them, since they're tagged error no tool want 
them as an input. If I could, I would just ignore the issue.




7 - If you load the BAM file at the public Galaxy web site (using 
FTP), the load is successful and the BAM file once imported into a 
history appears OK? Please share link from this test in case we need 
to examine. (Options - Share or Publish, generate link, email to me 
and I can share with dev team if needed).


If you mean when the data is actually copied in Galaxy, yes everything 
works fine since the grooming is perform during the upload process.


I never tried the public instance though. If you need me to share one of 
the files with you there, I'll have to ask for permission first, since 
the data's not mine.




Thanks for providing more info or perhaps you will find that one of 
these uncovers the issue,


Thanks for your help :)

Regards,
L-A



Best,

Jen
Galaxy team

On 7/18/11 2:05 AM, Louise-Amélie Schmitt wrote:

Hello everyone

Whenever we try to load BAM files without copying them, we get an error
stating the files need grooming, and can't use them at all.

Is it this serious? Would there be a way to bypass that?

Thanks!
L-A
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[galaxy-user] How to delete multiple items in libraries?

2011-06-20 Thread Louise-Amélie Schmitt 

Hello everyone

In the admin panel  Manage data libraries section I have an issue with 
deleting datasets.


When I click on each dataset's triangle menu and ask for deletion, 
everything is fine. But whenever I select datasets and ask for deletion 
with the drop down menu at the bottom of the page, Galaxy tells me I 
don't have the rights to delete them.


I get the following message:
You are not authorized to delete any of the selected datasets.

Did I miss anything?

Thanks,
L-A
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Re: [galaxy-user] How to delete multiple items in libraries?

2011-06-20 Thread Louise-Amélie Schmitt 

Ok no problem :)

Thanks a lot

L-A

Le 20/06/2011 17:50, Greg Von Kuster a écrit :

Hello Louise-Amelie,

This behavior was corrected in change set 5612:3297ec86d657, which 
should be available in the distribution within the next week or so. 
 Sorry for the inconvenience.


Greg Von Kuster


On Jun 20, 2011, at 11:06 AM, Louise-Amélie Schmitt wrote:


Hello everyone

In the admin panel  Manage data libraries section I have an issue 
with deleting datasets.


When I click on each dataset's triangle menu and ask for deletion, 
everything is fine. But whenever I select datasets and ask for 
deletion with the drop down menu at the bottom of the page, Galaxy 
tells me I don't have the rights to delete them.


I get the following message:
You are not authorized to delete any of the selected datasets.

Did I miss anything?

Thanks,
L-A
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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu mailto:g...@bx.psu.edu





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Re: [galaxy-user] New Galaxy User

2011-06-16 Thread Louise-Amélie Schmitt 

Hi

1 - You might want to read the bitbucket wiki instead: 
https://bitbucket.org/galaxy/galaxy-central/wiki/Home
There you can find all the information you will need to understand the 
configuration files, but don't expect a detailed description of the 
whole directory structure. The information is divided in topics. It's 
easier to understand that way anyway.


2 - If you mean the prerequisites, you might just need an appropriate 
version of python. (since you already have mercurial)
If you mean the software behind each tool, it has to be in the $PATH of 
the user running Galaxy.

If you mean the eggs, Galaxy will do it for you.

Hope that helps :) (hopefully I didn't forget anything, lack of sleep is 
a pain)


Regards,
L-A


Le 16/06/2011 13:14, gaurav thareja a écrit :

Hi All,
I am a new user of Galaxy. I am trying to configure galaxy on my local 
system. I took clone of 
repository(https://bitbucket.org/galaxy/galaxy-dist). But I have 
couple of issues while understanding code base:


   1. Is there any help file explaining directory structure and what
  all configuration files used for?
   2. I got list of all dependencies from website, Do I have to
  install all tools in /usr/local/bin/ or can be installed at any
  custom location?

I have already gone through tutorial 
(http://gmod.org/wiki/Galaxy_Tutorial) which was quite helpful and 
interesting but doesn't quite talk about my doubts above.


Regards

Gaurav Thareja



--
Regards

Gaurav Thareja


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Re: [galaxy-user] Most Popular Linux flavour for Galaxy

2011-06-07 Thread Louise-Amélie Schmitt 

Hi,

Our local instance runs on CentOS 5 and is happy with it :)
We didn't have the choice though.

Regards
L-A

Le 07/06/2011 14:00, Matloob Khushi a écrit :


Hello Galaxy Users

We are anticipating setting up a local instance of Galaxy and 
wondering what is the most popular (or best) flavour of Linux people 
out there using.


I wonder which OS on UseGalaxy.org has been used. Thanks for your help.

Regards
Matloob
PhD Candidate


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[galaxy-user] suggestion for multithreading

2011-04-19 Thread Louise-Amélie Schmitt 
Hello everyone,

I'm using TORQUE with Galaxy, and we noticed that if a tool is
multithreaded, the number of needed cores is not communicated to pbs,
leading to job crashes if the required resources are not available when
the job is submitted.

Therefore I modified a little the code as follows in
lib/galaxy/jobs/runners/pbs.py

256 # define PBS job options
257 attrs.append( dict( name = pbs.ATTR_N, value = str( %s_%s_%
s % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user ) ) ) )
258 mt_file = open('tool-data/multithreading.csv', 'r')
259 for l in mt_file:
260 l = string.split(l)
261 if ( l[0] == job_wrapper.tool.id ):
262 attrs.append( dict( name = pbs.ATTR_l,
resource = 'nodes', value = '1:ppn='+str(l[1]) ) )
263 attrs.append( dict( name = pbs.ATTR_l,
resource = 'mem', value = str(l[2]) ) )
264 break
265 mt_file.close()
266 job_attrs = pbs.new_attropl( len( attrs ) +
len( pbs_options ) )

(sorry it didn't come out very well due to line breaking)

The csv file contains a list of the multithreaded tools, each line
containing:
tool id\tnumber of threads\tmemory needed\n

And it works fine, the jobs wait for their turn properly, but
information is duplicated. Perhaps there would be a way to include
something similar in galaxy's original code (if it is not already the
case, I may not be up-to-date) without duplicating data.

I hope that helps :)

Best regards,
L-A

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