Hi John, I can confirm you that your advice putting "LWR_CURL_TRANSPORT=1" works very fine, thanks a lot! Sorry, i haven't expressed myself correctly for my second question, thanks for answering, it helps me. I have another problem with LWR, when executing the jobs on the Windows Server, i have the following bug (it happens a lot of time, and i must restart the LWR server in order for it to works): File "C:\Python2764\lib\site-packages\paste-1.7.5.1-py2.7.egg\paste\httpserver py", line 287, in wsgi_execute self.wsgi_start_response) File "C:\Desktop\lwr_master\lwr\web\framework.py", l ne 37, in __call__ return controller(environ, start_response, **request_args) File "C:\Desktop\lwr_master\lwr\web\framework.py", l ne 141, in controller_replacement resp = self.__build_response(result) File "C:\Desktop\lwr_master\lwr\web\framework.py", l ne 129, in __build_response resp = Response(body=self.body(result)) File "C:\Desktop\lwr_master\lwr\web\framework.py", l ne 155, in body body = dumps(result) File "C:\Python2764\lib\json\__init__.py", line 243, in dumps return _default_encoder.encode(obj) File "C:\Python2764\lib\json\encoder.py", line 207, in encode chunks = self.iterencode(o, _one_shot=True) File "C:\Python2764\lib\json\encoder.py", line 270, in iterencode return _iterencode(o, 0) nicodeDecodeError: 'utf8' codec can't decode byte 0x92 in position 718: invalid start byte Bests regards and thank you very much for your help, Misharl Monsoor. Le 21/11/2014 17:44, John Chilton a écrit :
On Wed, Nov 19, 2014 at 12:58 PM, Misharl Monsoor <mmonsoor@sb-roscoff.fr> wrote:
Hi John ,
First all, thank you very much for your quick reply. I will test your suggestion about pycurl, and tell you if it has worked. For the second question, i was wondering if it is possible with LWR to define a path (where are located the inputs) as an input (string input in the wrapper xml). Still not certain I understand - but I do not believe this is possible for datasets - this is something that must be configured for the LWR itself. If you have inputs to the tool that are not datasets - such as reference or index data - those could potentially be specified this way as just <data type="text"... in your tool. Those parameters will be passed through on the command-line just like any other parameter.
Hope this helps. -John
Thank you again for your help,
Misharl Monsoor.
Le 19/11/2014 15:30, John Chilton a écrit :
If you install pycurl (globally or in a Galaxy's virtualenv) and set LWR_CURL_TRANSPORT=1 in Galaxy's environment than the LWR will stream large files with CURL instead of the mmap hack.
I don't understand your second question - the LWR should stream whatever data inputs are selected by the user. If you want the tool to be able to take many inputs you can use multiple="true" on your data parameter or use a repeat block. (https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax).
Hope this helps, -John
On Mon, Nov 17, 2014 at 3:04 AM, Misharl Monsoor <mmonsoor@sb-roscoff.fr> wrote:
Hi everybody,
In our lab, we are trying to connect our Galaxy instance to a Windows 7 64 bits server, in order to executes programs that need to be run within Windows. However we have a problem concerning the size of the input that is uploaded to the Windows server, it doesn't accept inputs with a size > 1.3 Gb ? We have the following problem with mmap function:
data = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ) error: [Errno 12] Cannot allocate memory
I have another question concerning the inputs, is there a way to use several inputs that be uploaded to a Windows Server?
Thank you very much in advance,
Bests regards,
Cheers,
Misharl Monsoor ___________________________________________________________ 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: http://lists.bx.psu.edu/
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