Toqa,

Just to make sure I've understood your question: the problem is that a tool 
that you're trying to wrap doesn't provide a way to specify a particular output 
filename?  Take a look at the from_work_dir attribute of a <data> element.

Or are you asking how to define outputs in general?  For that, see the wiki at 
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coutputs.3E_tag_set

Lastly, for new questions please start new email threads, instead of replying 
to old ones.  This makes it much easier for us to track our responses and make 
sure people get appropriate help.

-Dannon


On Dec 5, 2011, at 1:26 PM, Toqa Manasrah wrote:

> Hi Everybody,
> I am running a tool which is not defining the output file name as parameter.
> the tool is running and I can see the output file in the history directory 
> but not in the history frame.
> 
> how could I solve the problem? I should see and download the output file from 
> the history but I see an error message instead. the error message not a real 
> error but rather galaxy cannot figure out which file to display?
> 
> your help is appreciated,
> 
> 
> ________________________________________
> From: Jennifer Jackson [j...@bx.psu.edu]
> Sent: Tuesday, November 08, 2011 8:22 AM
> To: Toqa Manasrah
> Cc: Galaxy Dev
> Subject: Re: [galaxy-dev] Installing Galaxy on local server
> 
> Hello Tuqa,
> 
> Galaxy will not stop by itself. That said, you will want to monitor the
> instance and any associated cluster, just as you would any other
> important processes.
> 
> Please send all follow-up with a cc to the mailing list ("reply-all").
> The development community is a great resource for administrative advice
> and they may have more to add to this reply, i.e. how stable they have
> found Galaxy to be under various conditions.
> 
> Best,
> 
> Jen
> Galaxy team
> 
> On 11/8/11 4:01 AM, Toqa Manasrah wrote:
>> Thank you so much,
>> 
>> I did the installation and I ran it under my server.
>> I have one thing concerning about now. if u can help plz.
>> 
>> how to run Galaxy in such way that the html interface will continuously 
>> working and available for all users visiting the page?
>> 
>> i mean how to guarantee that the "sh run.sh" will keep running without any 
>> interrupt?
>> 
>> Thank you,
>> Tuqa
>> 
>> ________________________________________
>> From: Jennifer Jackson [j...@bx.psu.edu]
>> Sent: Thursday, November 03, 2011 6:47 PM
>> To: Toqa Manasrah
>> Cc: galaxy-...@bx.psu.edu
>> Subject: Re: [galaxy-dev] Installing Galaxy on local server
>> 
>> Hello Toqa,
>> 
>>  From your description, this sounds like a local installation for the
>> Galaxy instance itself. Then you can add on a cluster (local or cloud)
>> as needed.
>> 
>> Help is under "Deploy Galaxy" at http://wiki.g2.bx.psu.edu/
>> Also see the "Tool Shed" at http://wiki.g2.bx.psu.edu/Tool%20Shed
>> 
>> Hopefully the documentation is helpful,
>> 
>> Best,
>> 
>> Jen
>> Galaxy team
>> 
>> On 11/3/11 9:40 AM, Toqa Manasrah wrote:
>>> Hello,
>>> 
>>> I am a graduate student at GSU. I am looking for installing GALAXY on
>>> our local server http://alla.cs.gsu.edu/~software. as a result I like my
>>> server homepage start with the GALAXY interface, like this one:
>>> http://rna1.engr.uconn.edu:7474/ . after that I wish to integrate some
>>> software tolls that we developed in ourdepartment. my primary question
>>> is which option Ihave to choose: Local or cloud?
>>> 
>>> looking forward for your help and directions.
>>> 
>>> Thank you.
>>> 
>>> Tuqa
>>> 
>>> 
>>> 
>>> ___________________________________________________________
>>> 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/
>> 
>> --
>> Jennifer Jackson
>> http://usegalaxy.org
>> http://galaxyproject.org/wiki/Support
>> 
> 
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/wiki/Support
> 
> ___________________________________________________________
> 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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