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 [dannonba...@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 [dannonba...@me.com]
Sent: Monday, December 05, 2011 1:54 PM
To: Toqa Manasrah
Cc: galaxy-...@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 [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,
