Hello Nate,

I just tried the modal upload dialog and it says "File exceeds 2GB. Please use 
FTP client".
Is there a way to increase that file size limitation?

Cordialement / Regards,
Edgar Fernandez

De : Nate Coraor [mailto:n...@bx.psu.edu]
Envoyé : January-22-15 12:02 PM
À : Fernandez Edgar
Cc : John Chilton; galaxy-...@bx.psu.edu
Objet : Re: [galaxy-dev] galaxy and torque - resource allocation

Hi Edgar,

Please make sure you have disabled the developer options `use_interactive` and 
`debug` in galaxy.ini, then restart your Galaxy server and try the upload again.

Also, please try out the modal upload dialog as I suggested, it should prevent 
a "stuck" upload in the future.

--nate



On Thu, Jan 22, 2015 at 10:25 AM, Fernandez Edgar 
<edgar.fernan...@umontreal.ca<mailto:edgar.fernan...@umontreal.ca>> wrote:
Hello Nate,


Thank you for answer so quickly.
My apache logs (/var/log/httpd/galaxy-prod-access_log) looks like this
ip_addr - - [22/Jan/2015:10:17:31 -0500] "POST 
/galaxy-prod/tool_runner/upload_async_create HTTP/1.1" 200 37
ip_addr - - [22/Jan/2015:10:17:32 -0500] "GET 
/galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 235
ip_addr - - [22/Jan/2015:10:17:32 -0500] "GET 
/galaxy-prod/tool_runner/upload_async_message HTTP/1.1" 200 1401
ip_addr - - [22/Jan/2015:10:17:36 -0500] "GET 
/galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 235
ip_addr - - [22/Jan/2015:10:17:40 -0500] "GET 
/galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 235
ip_addr - - [22/Jan/2015:10:17:44 -0500] "GET 
/galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 235
ip_addr - - [22/Jan/2015:10:17:48 -0500] "GET 
/galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 235

And my galaxy logs (/home/galaxy/galaxy-prod/config/main.log):
ip_addr - - [22/Jan/2015:10:17:31 -0400] "POST 
/galaxy-prod/tool_runner/upload_async_create HTTP/1.1" 200 - 
"http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0 (X11; 
Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 
Safari/537.36"
ip_addr - - [22/Jan/2015:10:17:32 -0400] "POST /galaxy-prod/tool_runner/index 
HTTP/1.1" 500 - "http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; 
"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) 
Chrome/40.0.2214.91 Safari/537.36"
Error - <type 'exceptions.OverflowError'>: signed integer is greater than 
maximum
ip_addr - - [22/Jan/2015:10:17:32 -0400] "GET 
/galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - 
"http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0 (X11; 
Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 
Safari/537.36"
ip_addr - - [22/Jan/2015:10:17:32 -0400] "GET 
/galaxy-prod/tool_runner/upload_async_message HTTP/1.1" 200 - 
"http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0 (X11; 
Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 
Safari/537.36"
URL: http://esiservera.esi.umontreal.ca:8081/galaxy-prod/tool_runner/index
File '/home/galaxy/galaxy-prod/lib/galaxy/web/framework/middleware/error.py', 
line 149 in __call__
  app_iter = self.application(environ, sr_checker)
File 
'/home/galaxy/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', 
line 84 in __call__
  return self.application(environ, start_response)
File 
'/home/galaxy/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py',
 line 633 in __call__
  return self.application(environ, start_response)
File '/home/galaxy/galaxy-prod/lib/galaxy/web/framework/base.py', line 132 in 
__call__
  return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy-prod/lib/galaxy/web/framework/base.py', line 185 in 
handle_request
  kwargs = trans.request.params.mixed()
File 'build/bdist.linux-x86_64-ucs4/egg/webob/__init__.py', line 900 in params
File 'build/bdist.linux-x86_64-ucs4/egg/webob/__init__.py', line 892 in 
str_params
File 'build/bdist.linux-x86_64-ucs4/egg/webob/__init__.py', line 818 in str_POST
File '/usr/lib64/python2.6/cgi.py', line 508 in __init__
  self.read_multi(environ, keep_blank_values, strict_parsing)
File '/usr/lib64/python2.6/cgi.py', line 635 in read_multi
  headers = rfc822.Message(self.fp)
File '/usr/lib64/python2.6/rfc822.py', line 108 in __init__
  self.readheaders()
File '/usr/lib64/python2.6/rfc822.py', line 155 in readheaders
  line = self.fp.readline()
File 
'/home/galaxy/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py', 
line 482 in readline
  data = self.file.readline(max_read)
File '/usr/lib64/python2.6/socket.py', line 415 in readline
  bline = buf.readline(size)
OverflowError: signed integer is greater than maximum


CGI Variables
-------------
  CONTENT_LENGTH: '2625522525<tel:2625522525>'
  CONTENT_TYPE: 'multipart/form-data; 
boundary=----WebKitFormBoundary9c9hOVrAGAXKJtdd'
  HTTP_ACCEPT: '*/*'
  HTTP_ACCEPT_ENCODING: 'gzip, deflate'
  HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.8'
  HTTP_CONNECTION: 'Keep-Alive'
  HTTP_COOKIE: 
'galaxysession=d122f4f53e5da72f16add67ded507460da12cda8c8b0781476c9ddbea84bd40a1e299b3d9b7a9e3a;
 
galaxysession=d122f4f53e5da72f439b77b098b6a77c8fe4c3cee6d2a1f587a8445290a468f305b3911dd27efa9e'
  HTTP_HOST: 
'esiservera.esi.umontreal.ca:8081<http://esiservera.esi.umontreal.ca:8081>'
  HTTP_ORIGIN: 'http://esiservera.esi.umontreal.ca:8081'
  HTTP_REFERER: 'http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root'
  HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, 
like Gecko) Chrome/40.0.2214.91 Safari/537.36'
  HTTP_X_REQUESTED_WITH: 'XMLHttpRequest'
  PATH_INFO: '/tool_runner/index'
  REMOTE_ADDR: 'ip_addr'
  REQUEST_METHOD: 'POST'
  SCRIPT_NAME: '/galaxy-prod'
  SERVER_NAME: 'esiservera.esi.umontreal.ca<http://esiservera.esi.umontreal.ca>'
  SERVER_PORT: '7112'
  SERVER_PROTOCOL: 'HTTP/1.1'


WSGI Variables
--------------
  application: <paste.recursive.RecursiveMiddleware object at 0x7fd1500e9b10>
  is_api_request: False
  paste.cookies: (<SimpleCookie: 
galaxysession='d122f4f53e5da72f439b77b098b6a77c8fe4c3cee6d2a1f587a8445290a468f305b3911dd27efa9e'>,
 
'galaxysession=d122f4f53e5da72f16add67ded507460da12cda8c8b0781476c9ddbea84bd40a1e299b3d9b7a9e3a;
 
galaxysession=d122f4f53e5da72f439b77b098b6a77c8fe4c3cee6d2a1f587a8445290a468f305b3911dd27efa9e')
  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 
0x7fd1500e9550>
  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 
0x7ef2850>
  paste.recursive.forward: <paste.recursive.Forwarder from /galaxy-prod>
  paste.recursive.include: <paste.recursive.Includer from /galaxy-prod>
  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from 
/galaxy-prod>
  paste.recursive.script_name: '/galaxy-prod'
  paste.throw_errors: True
  request_id: 'c93de906a24911e4bd5d002264f83610'
  webob._parsed_query_vars: (MultiDict([]), '')
  wsgi process: 'Multithreaded'
------------------------------------------------------------
ip_addr - - [22/Jan/2015:10:17:36 -0400] "GET 
/galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - 
"http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0 (X11; 
Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 
Safari/537.36"
ip_addr - - [22/Jan/2015:10:17:40 -0400] "GET 
/galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - 
"http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0 (X11; 
Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 
Safari/537.36"
ip_addr - - [22/Jan/2015:10:17:44 -0400] "GET 
/galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - 
"http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0 (X11; 
Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 
Safari/537.36"
ip_addr - - [22/Jan/2015:10:17:48 -0400] "GET 
/galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - 
"http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0 (X11; 
Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 
Safari/537.36"
ip_addr - - [22/Jan/2015:10:17:52 -0400] "GET 
/galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - 
"http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0 (X11; 
Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 
Safari/537.36"
ip_addr - - [22/Jan/2015:10:17:59 -0400] "GET 
/galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - 
"http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0 (X11; 
Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 
Safari/537.36"
ip_addr - - [22/Jan/2015:10:18:04 -0400] "GET 
/galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - 
"http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0 (X11; 
Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 
Safari/537.36"
ip_addr - - [22/Jan/2015:10:18:10 -0400] "GET 
/galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - 
"http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0 (X11; 
Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 
Safari/537.36"
ip_addr - - [22/Jan/2015:10:18:29 -0400] "GET 
/galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - 
"http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0 (X11; 
Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 
Safari/537.36"
ip_addr - - [22/Jan/2015:10:18:36 -0400] "GET 
/galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - 
"http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0 (X11; 
Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 
Safari/537.36"

However, I still see on my galaxy webpage the document in blue with the arrow 
going up constantly.

Do you think it’s an apache configuration error or galaxy or both?

Cordialement / Regards,
Edgar Fernandez

De : Nate Coraor [mailto:n...@bx.psu.edu<mailto:n...@bx.psu.edu>]
Envoyé : January-22-15 10:10 AM
À : Fernandez Edgar
Cc : John Chilton; galaxy-...@bx.psu.edu<mailto:galaxy-...@bx.psu.edu>

Objet : Re: [galaxy-dev] galaxy and torque - resource allocation

Hi Edgar,

I'd suggest checking your Apache logs to see if the upload was denied by the 
server configuration (possibly for being too large).

Also, please try using the modal upload method to see whether the upload is 
actually completing. This can be found by clicking the icon of a box with an up 
arrow at the top of the tool panel.

There are multiple steps to an upload - the first is sending the data to the 
server. After that, Galaxy creates a job and detects metadata about the 
uploaded dataset. Prior to the modal upload, a (purple "uploading") history 
item would be created as soon as the upload started, but if the transfer to the 
server was interrupted the history item may remain "stuck" in that state 
without providing feedback to the user that the upload was no longer 
progressing. The modal provides an upload progress bar, and only once all the 
data has been sent to the server does it create a history item (in the gray 
"queued") state.


On Thu, Jan 22, 2015 at 8:50 AM, Fernandez Edgar 
<edgar.fernan...@umontreal.ca<mailto:edgar.fernan...@umontreal.ca>> wrote:
Hello John,

This is totally excellent!
This gave me a great idea for my little torque installation.

I hope you don't mind but I have an unrelated issue with torque that I do not 
seem to grasp.
My issue is that it take a rediculious amount of time to upload a 2Gb file.
I tried many different configurations of apache to upload that 2Gb file without 
success.
Galaxy keeps showing that arrow going up constantly (over 12h).
And this is an upload from a file located on the server running galaxy.

Here is some information from my installation.
1. Server redhat6 with galaxy behind an Apache HTTP Server proxy like described 
on your website.
2. I have Apache HTTP Server running as the galaxy user with
        a. Serving Galaxy at a sub directory
        b. Compression and caching
        c. Sending files using Apache

You will see in attachment my apache's galaxy, deflate, expire and xsendfile 
configuration file.
Furthermore, I've changed the following in galaxy.ini:
        apache_xsendfile = True
        upstream_gzip = False

Any suggestions?
Any information I missed?
PLEASE HELP!!!

Cordialement / Regards,
Edgar Fernandez


-----Message d'origine-----
De : John Chilton [mailto:jmchil...@gmail.com<mailto:jmchil...@gmail.com>]
Envoyé : January-21-15 9:34 PM
À : Fernandez Edgar
Cc : galaxy-...@bx.psu.edu<mailto:galaxy-...@bx.psu.edu>
Objet : Re: [galaxy-dev] galaxy and torque - resource allocation

Was hoping someone with an actual torque cluster would respond. I think the way 
you would configure this might be for instance might be setting 
native_specification like "-l nodes=1:ppn=n". Depending on how things are 
configured or simply because I am ignorant - this may be wrong - but I think 
what you really want should look a lot like your arguments to qsub. So let say 
you have defined a job runner plugin called pbs_drmaa at the top of your 
job_conf.xml file. Then you could default everything to a single core by 
default and send "big" jobs to a destination with 8 cores with destinations and 
tool sections that look something like this...

...

  <destinations default="singlecore">
        <destination id="singlecore" runner="pbs_drmaa">
          <param id="native_specification">-l nodes=1:ppn=1</param>
        </destination>
        <destination id="multicore" runner="pbs_drmaa">
          <param id="native_specification">-l nodes=1:ppn=8</param>
        </destination>
  </destinations>

and ...

  <tools>
    <tool id="bowtie2" destination="multicore" />
    <tool id="bowtie" destination="multicore" />
    <tool id="deeptools" destination="multicore" />
    <tool id="cufflinks"destination="multicore" />
    <tool id="cuffdiff" destination="multicore" />
    <tool id="cuffmerge" destination="multicore" />
    <tool id="tophat2" destination="multicore" />
  </tools>

Again - that native specification could be wrong - probably best to test it out 
locally (or maybe Nate or JJ will step in and correct me).

Hope this helps,
-John


On Mon, Jan 19, 2015 at 8:05 AM, Fernandez Edgar 
<edgar.fernan...@umontreal.ca<mailto:edgar.fernan...@umontreal.ca>> wrote:
> Hello gents,
>
> Once again I would like to convey my most sincere appreciation for your 
> help!!!
> And yes I would like to hear your elaboration on my DRMAA runner which is 
> what I'm using.
> So my installation looks like: galaxy --> pbs_drmaa --> torque
>
> Cordialement / Regards,
> Edgar Fernandez
>
> -----Message d'origine-----
> De : John Chilton [mailto:jmchil...@gmail.com<mailto:jmchil...@gmail.com>] 
> Envoyé : January-18-15
> 8:59 PM À : Fernandez Edgar Cc : 
> galaxy-...@bx.psu.edu<mailto:galaxy-...@bx.psu.edu> Objet : Re:
> [galaxy-dev] galaxy and torque - resource allocation
>
> Galaxy generally defers to the DRM (torque in your case) for dealing with 
> these things. In your job_conf.xml you can specify limits for memory or CPUs 
> and Galaxy will pass these along to the DRM at which point it is up to the 
> DRM to enforce these - details depend on if you are using the PBS runner or 
> the DRMAA runner (let me know which and I can try to elobrate if that would 
> be useful).
>
> In your particular case - I don't believe torque "schedules" RAM so
> things will generally only be... throttled... by CPUs counts. This is
> what I was told by the admins at MSI when I worked there anyway. If
> you want to place hard limits on RAM I think you need to "upgrade" to
> the MOAB scheduler or switch over to a different DRM entirely like
> SLURM. Even for DRMs that deal more directly with memory - Galaxy
> doesn't provide a general mechanism for passing this along to the tool
> (https://trello.com/c/3RkTDnIn) - so it would be up to the tool to interact 
> with the environment variables your DRM sets .
>
> This sounds really terrible in the abstract - but it reality it usually isn't 
> an issue - most of Galaxy's multi-core mappers say have relatively low memory 
> per CPU usage - and for things like assemblers where this is more important - 
> one can usually just assign them to their own CPU or something like that to 
> ensure they get all the memory available.
>
> Unlike memory - Galaxy will attempt to pass the number of slots allocated to 
> a job to the tools by setting the GALAXY_SLOTS environment variable. All of 
> the multiple core devteam Galaxy tools at this point use this and so should 
> work - as should probably most multi-core tools from the tool shed - at least 
> the most popular ones.
>
> Hope this helps,
>
> -John
>
>
> On Tue, Jan 13, 2015 at 11:52 AM, Fernandez Edgar 
> <edgar.fernan...@umontreal.ca<mailto:edgar.fernan...@umontreal.ca>> wrote:
>> Hello gents,
>>
>>
>>
>> Hope everyone had a great holiday break!
>>
>> Wish you guys all the best for 2015!
>>
>>
>>
>> I have a couple of questions about how resources (CPU and memory) is
>> allocated when you have a galaxy and torque installation.
>>
>>
>>
>> So I’ve setup torque with some default and maximum amount of CPU and
>> memory allocations.
>>
>> However, I have some worries when it comes to application (like
>> tophat for example).
>>
>> By default, it takes half the CPU of a server unless specified otherwise.
>>
>> How is the CPU allocation is specified to application like tophat
>> through galaxy?
>>
>>
>>
>> Also, how does galaxy react if a job needs more memory than the limit
>> set by torque?
>>
>>
>>
>> Any information would help me a lot!
>>
>>
>>
>> My sincere salutations to you all!!!
>>
>>
>>
>> Cordialement / Regards,
>>
>>
>>
>> Edgar Fernandez
>>
>> System Administrator (Linux)
>>
>> Direction Générale des Technologies de l'Information et de la
>> Communication
>>
>> (  Bur. : 1-514-343-6111<tel:1-514-343-6111> poste 16568
>>
>>
>>
>> Université de Montréal
>>
>> PAVILLON ROGER-GAUDRY, bureau X-218
>>
>>
>>
>>
>> ___________________________________________________________
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