Re: [galaxy-dev] HMMER wrappers

[Edward Kirton]

i created a new toolshed repo, hmmer since i couldn't rename it.  as
suggested, it has the hmmscan/hmmsearch as one tool, plus hmmpress.  will
add hmmbuild, hmmalign asap; others upon request.

dave, is there a way to delete an old tool?  (hmmscan)

On Wed, Feb 29, 2012 at 10:12 AM, Edward Kirton  wrote:

> great suggestion; i'll make those changes
>
> On Wed, Feb 29, 2012 at 10:05 AM, Peter Cock wrote:
>
>> On Wed, Feb 29, 2012 at 5:56 PM, Edward Kirton  wrote:
>> > hi, peter - i will fix the description and upload hmmsearch and infernal
>> > today.
>>
>> Great.
>>
>> Assuming hmmscan and hmmsearch have (almost) the same command
>> line API, there is something to be said for presenting them as one tool
>> in Galaxy, with a drop down selection between them (with help text
>> about which is recommend adapted from the HMMER blog post). One
>> could even have an automatic selection by a wrapper script based on
>> the number of query sequences and the number of HMMs. My thinking
>> here is the detail of hmmscan vs hmmsearch is purely an implementation
>> detail that the end user shouldn't have to worry about.
>>
>> Or just duplicate most of the XML code and have two wrappers. But
>> as far as I know there isn't (yet) a nice way of reusing XML snippets
>> between tool wrappers... which would be handy.
>>
>> Thanks,
>>
>> Peter
>>
>
>
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[galaxy-dev] BOSC 2012 Call for Abstracts

[Brad Chapman]

Call for Abstracts for the 13th Annual Bioinformatics Open Source Conference 
(BOSC 2012)
A Special Interest Group (SIG) of ISMB 2012

Dates: July 13-14, 2012
Location: Long Beach, California
Web site: http://www.open-bio.org/wiki/BOSC_2012
Email: b...@open-bio.org
BOSC announcements mailing list:  
http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:
April 13, 2012: Deadline for submitting abstracts
May 7, 2012: Notification of accepted talk abstracts emailed to authors
July 11-12, 2012: Codefest 2012 programming session
July 13-14, 2012: BOSC 2012
July 15-17, 2012: ISMB 2012

The Bioinformatics Open Source Conference (BOSC) is sponsored by the
Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated
to promoting the practice and philosophy of Open Source software
development within the biological research community. To be considered
for acceptance, software systems representing the central topic in a
presentation submitted to BOSC must be licensed with a recognized Open
Source License, and be freely available for download in source code
form.

We invite you to submit one-page abstracts for talks and posters.  This year's 
session topics are:
- Cloud and Parallel Computing
- Linked Data
- Genome-scale Data Management
- Data Visualization and Imaging
- Translational Bioinformatics
- Software Interoperability (possibly a joint session with BSI-SIG,
  the Bioinformatics Software Interoperability SIG)
- Bioinformatics Open Source Project Updates
- Interfacing with Industry (panel)

Thanks to generous sponsorship from Eagle Genomics and an anonymous
donor, we are pleased to announce a competition for three Student
Travel Awards. Each winner will be awarded $250 to defray the costs of
travel to BOSC 2012.

For instructions on submitting your abstract, please visit
http://www.open-bio.org/wiki/BOSC_2012#Submitting_Abstracts

BOSC 2012 Organizing Committee:
Nomi Harris (chair), Jan Aerts, Brad Chapman, Peter Cock, Chris Fields, Erwin 
Frise, Peter Rice
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Re: [galaxy-dev] uploads stuck in history

[Luciano Cosme]

Hi,
  I was trying to upload data again and here is the error message that I
get:

Can't create peek [Errno 2] No such file or directory:
'/home/koala2/galaxy-dist/database/files/000/dataset_24.dat'




Exception happened during processing of request from ('127.0.0.1', 52338)
Traceback (most recent call last):
  File
"/home/koala2/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 1053, in process_request_in_thread
self.finish_request(request, client_address)
  File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib/python2.7/SocketServer.py", line 639, in __init__
self.handle()
  File
"/home/koala2/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 432, in handle
BaseHTTPRequestHandler.handle(self)
  File "/usr/lib/python2.7/BaseHTTPServer.py", line 343, in handle
self.handle_one_request()
  File
"/home/koala2/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 427, in handle_one_request
self.wsgi_execute()
  File
"/home/koala2/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 287, in wsgi_execute
self.wsgi_start_response)
  File "/home/koala2/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py",
line 202, in __call__
return app(environ, start_response)
  File
"/home/koala2/galaxy-dist/lib/galaxy/web/framework/middleware/xforwardedhost.py",
line 21, in __call__
return self.app( environ, start_response )
  File
"/home/koala2/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/config.py",
line 164, in __call__
app_iter = self.application(environ, start_response)
  File
"/home/koala2/galaxy-dist/lib/galaxy/web/framework/middleware/translogger.py",
line 68, in __call__
return self.application(environ, replacement_start_response)
  File
"/home/koala2/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py",
line 226, in __call__
return self.respond(environ, start_response)
  File
"/home/koala2/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py",
line 399, in respond
if self.xmlhttp_key in req.params:
  File
"/home/koala2/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg/webob/__init__.py",
line 900, in params
params = self.str_params
  File
"/home/koala2/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg/webob/__init__.py",
line 892, in str_params
return NestedMultiDict(self.str_GET, self.str_POST)
  File
"/home/koala2/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg/webob/__init__.py",
line 818, in str_POST
keep_blank_values=True)
  File "/usr/lib/python2.7/cgi.py", line 508, in __init__
self.read_multi(environ, keep_blank_values, strict_parsing)
  File "/usr/lib/python2.7/cgi.py", line 632, in read_multi
environ, keep_blank_values, strict_parsing)
  File "/usr/lib/python2.7/cgi.py", line 510, in __init__
self.read_single()
  File "/usr/lib/python2.7/cgi.py", line 647, in read_single
self.read_lines()
  File "/home/koala2/galaxy-dist/lib/galaxy/web/framework/base.py", line
268, in read_lines
self.read_lines_to_outerboundary()
  File "/usr/lib/python2.7/cgi.py", line 697, in read_lines_to_outerboundary
line = self.fp.readline(1<<16)
  File
"/home/koala2/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 467, in readline
data = self.file.readline(self.length - self._consumed)
  File "/usr/lib/python2.7/socket.py", line 412, in readline
bline = buf.readline(size)
OverflowError: signed integer is greater than maximum



On Mon, Mar 5, 2012 at 3:24 PM, Luciano Cosme wrote:

> I had same issue recently. I tried to upload files locally and give same
> error (from 50Mb or 17Gb as admin). The files never finish uploading. A few
> days ago I tried to upload around 20 files (up to 200Mb), most of them
> uploaded normally, but some wouldn't. I will try a different browser them
> Thanks.
>
>
>
> > 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /root/tool_menu
> HTTP/1.1" 200 - "http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux
> x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>
>
>
>
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Re: [galaxy-dev] uploads stuck in history

[Luciano Cosme]

I had same issue recently. I tried to upload files locally and give same
error (from 50Mb or 17Gb as admin). The files never finish uploading. A few
days ago I tried to upload around 20 files (up to 200Mb), most of them
uploaded normally, but some wouldn't. I will try a different browser them
Thanks.


> 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /root/tool_menu HTTP/1.1"
200 - "http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"


Luciano
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Re: [galaxy-dev] Defining Job Runners Dynamically

[Tony Raymond]

Hi Nate,

Has there been any progress on this? This enhancement would actually be very 
useful for our local Galaxy instance.

Cheers,
Tony

-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nate Coraor
Sent: Wednesday, January 25, 2012 10:56 AM
To: John Chilton
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Defining Job Runners Dynamically

Hey John,

This hasn't been forgotten.  I appreciate the code submission, and will review 
it as soon as possible.  I also created a relevant issue in Bitbucket:

https://bitbucket.org/galaxy/galaxy-central/issue/709/add-more-control-over-where-jobs-run

--nate

On Oct 15, 2011, at 10:42 PM, John Chilton wrote:

> Hello All,
> 
>   I just issued a pull request that augments Galaxy to allow defining job 
> runners dynamically at runtime 
> (https://bitbucket.org/galaxy/galaxy-central/pull-request/12/dynamic-job-runners).
>  Whether it makes the cut or not, I thought I would describe enhancements 
> here in case anyone else would find it useful.
> 
>   There a couple use cases we hope this will help us address for our 
> institution - one is dynamically switching queues based on user (we have a 
> very nice shared memory resource that can only be used by researchers with 
> NIH funding) and the other is inspecting input sizes to give more accurate 
> max walltimes to pbs (a small number of cufflinks jobs for instance take over 
> three days on our cluster but defining max walltimes in excess of that for 
> all jobs could result in our queue sitting idle around our monthly 
> downtimes). You might also imagine using this to dynamically switch queues 
> entirely based on input sizes or parameters, or alter queue priorities based 
> on the submitting user or input sizes/parameters.
> 
>   There are two steps to use this - you must add a line in universe.ini and 
> define a function to compute the true job runner string in the new file 
> lib/galaxy/jobs/rules.py. 
> 
>   This first step is similar to what you would do to statically assign a tool 
> to a particular job runner. If you would like to dynamically assign a job 
> runner for cufflinks you would start by adding a line like one of the 
> following to universe.ini
> 
> cufflinks = dynamic:///python
> -or-
> cufflinks = dynamic:///python/compute_runner
> 
> If you use the first form, a function called cufflinks must be defined in 
> rules.py, adding the extra argument after python/  lets you specify a 
> particular function by name (compute_runner in this example). This second 
> option could let you assign job runners with the same function for multiple 
> tools.
> 
> The only other step is to define a python function in rules.py that produces 
> a string corresponding to a valid job runner such as "local:///" or 
> "pbs:///queue/-l walltime=48:00:00/". 
> 
> If the functions defined in this file take in arguments, these arguments 
> should have names from the follow list: job_wrapper, user_email, app, job, 
> tool, tool_id, job_id, user. The plumbing will map these arguments to the 
> implied galaxy object. For instance, job_wrapper is the JobWrapper instance 
> for the job that gets passed to the job runner, user_email is the user's 
> email address or None, app is the main application configuration object used 
> throughout the code base that can be used for instance to get values defined 
> in universe.ini, job, tool, and user are model objects, and job_id and 
> tool_id the relevant ids.
> 
> If you are writing a function that routes a certain list of users to a 
> particular queue or increases their priority, you will probably only need to 
> take in one argument - user_email. However, if you are going to look at input 
> file sizes you may want to take in an argument called job and use the 
> following piece of code to find the input size for input named "input1" in 
> the tool xml. 
> 
> inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] 
> )
> inp_data.update( [ ( da.name, da.dataset ) for da in 
> job.input_library_datasets ] )
> input1_file = inp_data[ "input1" ].file_name
> input1_size = os.path.getsize( input1_file )
> 
> This whole concept works for a couple of small tests on my local machine, but 
> there are certain aspects of the job runner code that makes me feel there may 
> be corner cases I am not seeing where this approach may not work - so your 
> millage may vary.
> 
> -John
> 
>  
> John Chilton 
> Software Developer 
> University of Minnesota Supercomputing Institute 
> Office: 612-625-0917 
> Cell: 612-226-9223 
> E-Mail: chil...@msi.umn.edu 
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__

Re: [galaxy-dev] uploads stuck in history

[Nate Coraor]

By any chance, do you all happen to be using the nginx upload module?  I am 
guessing not.

--nate

On Feb 23, 2012, at 3:16 AM, Bossers, Alex wrote:

> I confirm the same strange behaviour since some of the last updates on the 
> central version. We are at the latest now. 
> It is also with medium (10Mb+ tarballs) AND large files! Furthermore its 
> seems to be in FireFox only They upload fine using IE8 or 9. Didn't test 
> other browsers though.
> 
> Annoying it is indeed.
> 
> Alex
> 
> 
> -Oorspronkelijk bericht-
> Van: galaxy-dev-boun...@lists.bx.psu.edu 
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Jorrit Boekel
> Verzonden: woensdag 22 februari 2012 10:15
> Aan: galaxy-dev@lists.bx.psu.edu
> Onderwerp: [galaxy-dev] uploads stuck in history
> 
> Dear list,
> 
> I have stumbled on some strange behaviour when uploading files to galaxy via 
> the upload.py tool. At times, the upload seems to be stalled in history and 
> is never actually performed, followed by a seemingly infinite history update 
> (see log below). My system is Ubuntu 11.10 and runs Python 2.7.2. I find the 
> behaviour in both my own modified galaxy install (based on galaxy-dist), and 
> in a fresh clone from galaxy-central.
> 
> I have tried to upload different files, and all seem to sometimes trigger the 
> behaviour, but not all the time. A restart of galaxy sometimes sorts things 
> out. Common for the debug messages is that it seems there is never a job id 
> generated as in "galaxy.tools.actions.upload_common INFO 2012-02-22 
> 10:06:36,186 tool
> upload1 created job id 2".
> 
> Has anyone seen similar things or can it be a problem with my system?
> 
> cheers,
> jorrit
> 
> 
> 
> 
> 
> 
> --Debug messa:
> 
> galaxy.web.framework DEBUG 2012-02-22 09:47:43,730 Error: this request 
> returned None from get_history(): http://localhost:8080/
> 127.0.0.1 - - [22/Feb/2012:09:47:43 +0200] "GET / HTTP/1.1" 200 - "-" 
> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 
> Firefox/10.0.2"
> 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /root/tool_menu HTTP/1.1" 200 
> - "http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; 
> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
> 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /history HTTP/1.1" 200 - 
> "http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
> 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "POST /root/user_get_usage 
> HTTP/1.1" 200 - "http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; 
> Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
> 127.0.0.1 - - [22/Feb/2012:09:47:50 +0200] "GET
> /tool_runner?tool_id=upload1 HTTP/1.1" 200 - 
> "http://localhost:8080/root/tool_menu"; "Mozilla/5.0 (X11; Ubuntu; Linux 
> x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "POST 
> /tool_runner/upload_async_create HTTP/1.1" 200 - "http://localhost:8080/"; 
> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "GET 
> /tool_runner/upload_async_message HTTP/1.1" 200 - "http://localhost:8080/"; 
> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "GET /history HTTP/1.1" 200 - 
> "http://localhost:8080/tool_runner/upload_async_message"; "Mozilla/5.0 (X11; 
> Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "POST /root/user_get_usage 
> HTTP/1.1" 200 - "http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; 
> Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
> 127.0.0.1 - - [22/Feb/2012:09:48:13 +0200] "GET
> /tool_runner?tool_id=upload1 HTTP/1.1" 200 - 
> "http://localhost:8080/root/tool_menu"; "Mozilla/5.0 (X11; Ubuntu; Linux 
> x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
> 127.0.0.1 - - [22/Feb/2012:09:48:15 +0200] "POST /root/history_item_updates 
> HTTP/1.1" 200 - "http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; 
> Linux x86_64;
> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
> 127.0.0.1 - - [22/Feb/2012:09:48:19 +0200] "POST /root/history_item_updates 
> HTTP/1.1" 200 - "http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; 
> Linux x86_64;
> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
> 127.0.0.1 - - [22/Feb/2012:09:48:23 +0200] "POST /root/history_item_updates 
> HTTP/1.1" 200 - "http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; 
> Linux x86_64;
> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
> 127.0.0.1 - - [22/Feb/2012:09:48:27 +0200] "POST /root/history_item_updates 
> HTTP/1.1" 200 - "http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; 
> Linux x86_64;
> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
> 127.0.0.1 - - [22/Feb/2012:09:48:31 +0200] "POST /root/history_item_updates 
> HTTP/1.1" 200 - "http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; 
> Linux x86_64;

[galaxy-dev] Production environment and Apache's sendfile

[Jennifer Jackson]

Hello,

I am going to forward you question to the galaxy-...@bx.psu.edu mailing 
list so that the development community can offer advice.


http://wiki.g2.bx.psu.edu/Support#Mailing_Lists
http://wiki.g2.bx.psu.edu/Mailing%20Lists#The_lists


Thanks,

Jen
Galaxy team

On 3/2/12 8:00 AM, Yuri D'Elia wrote:

Hi everyone. I've set up a galaxy production environment and it seems to be 
working.
I've identified a couple of issues though:

If I enable apache_xsendfile, the little "eye" icon ("Display data in browser") 
on each dataset stops working. I get the following instead:

The requested URL /datasets/7e93e3cf926fb2b3/display/ was not found on this 
server

My document root is not the same as the galaxy root (as suggested). Everything 
else seems to work. Is this a bug?

Second question:

I want to rotate the galaxy log file (as specified with paster.py serve 
--log-file. I can't find a way to reopen the logfile in galaxy without taking 
down the whole service, or a way to redirect the log to a pipe together while 
using --daemon.

I cannot let the file grow forever.
Any suggestions?

Thanks.

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--
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http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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Re: [galaxy-dev] [galaxy-user] snpEff: html report is not displaying after update

[Dannon Baker]

Hi Raj,

What's going on here is probably that the snpEff output is being sanitized by 
galaxy prior to display.  The data is all intact, and I've recently added a 
config option 'sanitize_all_html' in changeset 6788:e58a87c91bc4 that will 
allow you to disable this for your local instance.  If you update your local 
instance and set sanitize_all_html = False in your universe_wsgi.ini, you 
should see the expected output.

-Dannon

On Feb 22, 2012, at 3:36 PM, Jennifer Jackson wrote:

> Hello Raj,
> 
> This tool is from the Tool Shed and is maintained by the tool author. To 
> contact them about functionality or problems, go to the Tool Shed at 
> http://toolshed.g2.bx.psu.edu/, locate the repository (search by 'snpEff'), 
> click on the name, in the the top far right corner locate the pull down menu 
> "Repository Actions". Select "Contact repository owner" to send them a 
> message.
> 
> There have been many updates to Galaxy recently and it is possible that one 
> of these had an impact on this tool. I am going to send your email to 
> galaxy-...@bx.psu.edu, to see if anyone else has had problems with this tool 
> since the last distribution update.
> 
> You may be asked to provide more information (be as specific as you can): the 
> hg pull #, any customizations, python version, etc.
> 
> Regards,
> 
> Jen
> Galaxy team
> 
> On 2/14/12 8:28 PM, Praveen Raj Somarajan wrote:
>> Hi All,
>> 
>> I updated galaxy recently to the latest version. Everything looks fine,
>> except snpEff report html view. It was displaying properly (all tables
>> and summary values) before the update, but the summary values are not
>> displaying after the update. A sample screen-shot is attached for your
>> reference. Could you please figure out this issue?
>> 
>> When I ran the same on command line, the reports were generated
>> correctly. I assume, something (datatypes or preview) has changed by the
>> update. Please let me know the work around on this?
>> 
>> Secondly, as we know, snpEff also generates a gene-wise annotation file
>> along with other results, but somehow we cannot access this file through
>> Galaxy. Though we see the link in the html report, but it seems the path
>> is broken.
>> 
>> Let me know your suggestions.
>> 
>> Best,
>> 
>> Raj
>> 
>> 
>> 
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[galaxy-dev] Variable number of inputs in Workflow (or optional inputs)

[Jennifer Jackson]

Hello Daniel,

Examining existing tools that have multiple/optional inputs can be a 
good way to see how this is done. One example is the tool: "NGS: QC and 
manipulation -> Manipulate FASTQ".


The 'Manipulate FASTQ' tool source is here:
http://bitbucket.org/galaxy/galaxy-central/src/e58a87c91bc4/tools/fastq/

fastq_manipulation.py
fastq_manipulation.xml

The tool tag set is defined in this wiki;
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax

See , , and  for more details and examples.

Questions about tools are best sent to the galaxy-...@bx.psu.edu mailing 
list (the galaxy-user list is primarily for questions about data/tools 
usages on the main public instance). I am going to forward your question 
over there so that the development community can add to my reply in case 
they have a simpler way of doing this or other advice.


Best,

Jen
Galaxy team

On 3/5/12 7:32 AM, Daniel Sobral wrote:

Hi,

I wanted to build a workflow where the first step would be a tool that
can have a variable number of inputs (e.g. a series).
It seems that I need to predefine apriori the number of inputs to give
to the tool.

Is there a way to define the number of inputs at runtime?
E.g. a series-like input?

Thanks,
Daniel
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[galaxy-dev] functional test issue - PDF output file comparison

[Anne Pajon]

Dear All,

I have noticed that some output files of functional tests are of type PDF. When 
comparing the one produced by the tool and the one stored in test-data/, they 
obviously differ even if they visually look identical. 

Is there a better way to compare PDF files within Galaxy than using diff? If 
not, do you have experience or suggestion at solving these functional test 
failures?

Thanks a lot in advance.
Kind regards,
Anne.
--
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Cancer Research UK - Cambridge Research Institute
Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
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Re: [galaxy-dev] Problem with python ./scripts/make_egg_packager.py

[Nate Coraor]

On Feb 14, 2012, at 11:07 PM, Jose William Valero Velasquez wrote:

> Hi, 
> 
> I'm writing you because i'm trying to install galaxy in a server running suse 
>  behind a proxy, so i have to build the eggs like if the server were offline, 
> in the guide says that i should execute the command 
> ./scripts/make_egg_packager.py but i get the following error, and i don't 
> really understand whats happening:
> 
> File "scripts/make_egg_packager.py", line 21, in 
> 
> c = Crate()
> 
> TypeError: __init__() takes at least 2 arguments (1 given)

Hi William,

It looks like you're using a fairly old version of Galaxy?  I'd suggest 
downloading the latest from https://bitbucket.org/galaxy/galaxy-dist/ .  This 
problem has been fixed in newer versions.

--nate

> 
> 
> 
> I'd really apreciate your help to figure out how to solve this issue.
> 
> 
> 
> William Valero
> 
> Universidad Nacional de Colombia. 
> 
> 
> 
> 
> 
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[galaxy-dev] Progress indicators/feedback for long jobs on Galaxy

[Jennifer Jackson]

Hi Greg,

I am going to forward your email over to the galaxy-...@bx.psu.edu 
mailing list where the development community can provide feedback.



Best,

Jen
Galaxy team


On 3/4/12 3:26 PM, Greg Edwards wrote:

Hi,

This has been raised a number of times .. one issue is at ...

https://bitbucket.org/galaxy/galaxy-central/issue/250/progress-of-running-jobs

but seems to have been dropped from Open to On Hold. There was another
similar request in the issues list but I can't find it just now.

I'd be gald to know if anything is happening on the idea of simple
progress indicators. The first things that were raised by my "users"
were 1) Don't know how long a data upload is going to take, and b) Don't
know what's happening with my tool execution. (And these were both
operations of only 5-10 minutes or so, they'd go crazy with the multi-GB
uploads and hours-long runs I see reported here).


I've implemented my own email-based scheme on a AWS EC2 CloudMan Galay,
seems to be working ok. It uses an Ubuntu package "sendEmail", which is
a self-conatined simple SMTP email sender. It sends progress emails out
of the main Perl tool code, via a bash script,  every 1 to N minutes
(selectable), to an email address supplied by the user. The emails have
configurable subject and content with brief display of Start, Progress
(every N minutes) and Success/Failure termination status.

You have to jump through some hurdles. AWS thinks your'e a spammer and
blocks emails after a while ! but you can submit a request to get around
that.

If anyone's interested let me know.

Cheers,
Greg E


--
Greg Edwards,
Port Jackson Bioinformatics
gedwar...@gmail.com 



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[galaxy-dev] Dynamic feedback whilst setting tool-parameters in Galaxy web-interface

[Tim Dorscheidt]

Hi, 

I've been writing several wrapper-files for statistical tools, and I was 
wondering whether it was possible to enhance the tool-interface currently 
available in the Galaxy web-interface. Ideally, I am looking for options to 
already display (some) tool-feedback in the user-interface of a tool dependent 
on the dataset selected from the "history" and user-defined parameters. An 
example would be a graph re-drawing itself every time the user selects a 
different dataset or alters a parameter, but simple text-feedback that 
dynamically updates itself would be a great start already. The "execute" button 
is now the only way to run code on user-input, and this makes Galaxy a rather 
cumbersome environment in the case of tools that require many iterations (or 
just when playing around with parameters).

So far, the only limited example I've seen of such "dynamic feedback" is when 
the user select a matrix from her "history" and Galaxy is able to read the 
amount of columns, which strictly speaking is a form of generating immediate 
feedback on the basis of user-selected input, but of course I'd like to define 
the code myself that is run on the input and what sort of feedback is derived 
and displayed from this.

I have seen the new "visualizations" section of Galaxy, which indeed allows for 
some of this, but it is clearly separate from the standard tool-funcitonality 
of Galaxy, and it does not allow for workflows (whereas the above functionality 
does not clash with workflows, which simply needs to access the static version 
of the tool).

Any help would be greatly appreciated.

Tim Dorscheidt
Scientific Programmer
Biosystems Data Analysis group, SILS
University of Amsterdam


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[galaxy-dev] problems with display at UCSC

[Hans-Rudolf Hotz]

Hi everybody


This is kind of an embarrassing question, but I am struggling to get the 
"display at UCSC" to work.



Finally after several years, our sysadmin agreed to change the Apache 
configuration (which handles the authentication via LDAP) according to 
the configuration provided in the wiki:

http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy


So, I thought this was a piece of cake to make the "display at UCSC" 
work. I changed the following (in order to prevent broken links on our 
production server, I have currently restricted it to "mm7", which nobody 
is using in our institute):


in "universe_wsgi.ini", I have:  'ucsc_display_sites = main'

in "tool-data/shared/ucsc/ucsc_build_sites.txt", I have:
'main   http://genome.ucsc.edu/cgi-bin/hgTracks?mm7'



For history items with "format: bed, database: mm7" I get the link: 
"display at UCSC 'main'", eg:


http://galaxy.fmi.ch/datasets/13185/display_at/ucsc_main?redirect_url=http%3A%2F%2Fgenome.ucsc.edu%2Fcgi-bin%2FhgTracks%3Fdb%3Dmm7%26position%3Dchr1%3A11873-1655775%26hgt.customText%3D%25s&display_url=http%3A%2F%2Fgalaxy.fmi.ch%2Froot%2Fdisplay_as%3Fid%3D13185%26display_app%3Ducsc%26authz_method%3Ddisplay_at



If I click on it, I get the right UCSC page (ie: mm7 
chr1:chr1:11,873-1,655,775).

But I get the following error message on the top of the page:

"Expected 200 
http://galaxy.fmi.ch/root/display_as?id=13185&display_app=ucsc&authz_method=display_at: 
401 Authorization Required"




Our sysadmin insists this is a Galaxy error (ie wrong configuration in 
the Galaxy code), but I ran out of ideas what else would need changing 
in Galaxy to make the display work.


Is there anything else I need to adjust in addition to the two changes 
in "universe_wsgi.ini" and "ucsc_build_sites.txt"?  Or is the error (as 
I suspect) somewhere in the Apache configuration.


Thank you very much for any pointers which might get the display to work 
for us


Regards, Hans
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[galaxy-dev] Double setup

[Ian Porter (NBI)]

Hi All,

I was wondering if I could have some advice/ and if this is a workable solution.

Basically there is a requirement to have both AD and Local accounts to be able 
to use galaxy on a VM.

So I have setup apache to have the two URL's http://here.com/AD/ and 
http://here.com/Local/ to goto there relevant place with using the same galaxy 
backend files for both setups of galaxy but only having a different 
universe_wsgi.ini for the AD version and universe_local_wsgi.ini for the local, 
and the [filter:proxy-prefix] for both to have either AD or Local as there 
prefix filters.

It appears to work in that you are able to login to both, but was wondering if 
anyone is able to stop a fatal flaw in this setup because I have just set it up 
and not really used it.

Regards
Ian
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