[galaxy-dev] Urgent help needed

Dannon Baker dannonbaker at me.com
Tue Dec 6 11:09:06 EST 2011 

I don't know anything about the tool or parameters in question , but it looks like the expected output filename is well formatted enough that you can derive it from the input filename and parameters.

You could write a small python wrapper to grant you full control over manipulating output files and finding/renaming them as you like, or, you could maybe try something like (and I have not tried this at all myself and have no idea what your parameters mean)  from_work_dir="${input1}reads_l_${parameter1}_${parameter2}_CNTGS_DIST0_EM20.txt"

Good luck-

Dannon

On Dec 5, 2011, at 3:52 PM, Toqa Manasrah wrote:

> Thank you so much Dannon.
> I appreciate your help but I need some more clarification.
> 
> in the tool I am integrating (which is java classes) if the input parameters are
> 
> ./main.bash  eps0.3_40reads.fa  population10_ref.fa 15 6 120
> 
> Then teh output is in eps0.3_40reads_I_6_15_CNTGS_DIST0_EM20.txt
> 
> As u notice the output file name is not specified in teh command line, and actually I dont have the source files to go over this naming restriction.
> 
> how I can use from_work_dir attribute to tell galaxy this the file to display?
> 
> note: there are 11 output files and I am interested in this one only ..._CNTGS_DIST0_EM20.txt
> 
> 
> any other method to overcome such problem  
> 
> I have presentation tomorrwo. hope things will work fine.
> 
> Thank you,
> ________________________________________
> From: Dannon Baker [dannonbaker at me.com]
> Sent: Monday, December 05, 2011 2:41 PM
> To: Toqa Manasrah
> Subject: Re: [galaxy-dev]  Urgent help needed
> 
> Sure.  See the link in my previous email (http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax) and look for the <data> section for an explanation of the attributes available to you.  For an example of a tool that uses the from_work_dir element, see the cufflinks, cuff compare, top hat, or trinity wrappers in your galaxy install.
> 
> -Dannon
> 
> 
> On Dec 5, 2011, at 2:25 PM, Toqa Manasrah wrote:
> 
>> Thank you Dannon,
>> I mean the first choice. no way to specify the output name in tool and it has many putputs but I am intereseted in one only.
>> 
>> Actually I dont know to use this attribute from_work_dir and I cant find help. can u help plz?
>> 
>> ________________________________________
>> From: Dannon Baker [dannonbaker at me.com]
>> Sent: Monday, December 05, 2011 1:54 PM
>> To: Toqa Manasrah
>> Cc: galaxy-dev at bx.psu.edu dev; Jennifer Jackson; galaxy-user
>> Subject: Re: [galaxy-dev]  Urgent help needed
>> 
>> 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 [jen at 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 [jen at bx.psu.edu]
>>>> Sent: Thursday, November 03, 2011 6:47 PM
>>>> To: Toqa Manasrah
>>>> Cc: galaxy-dev at 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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