I am running a tool which is not defining the output file name as
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,
To: Toqa Manasrah
Cc: Galaxy Dev
Subject: Re: [galaxy-dev] Installing Galaxy on local server
Galaxy will not stop by itself. That said, you will want to monitor
instance and any associated cluster, just as you would any other
Please send all follow-up with a cc to the mailing list ("reply-all").
The development community is a great resource for administrative
and they may have more to add to this reply, i.e. how stable they have
found Galaxy to be under various conditions.
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
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.
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
./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
how I can use from_work_dir attribute to tell galaxy this the file to
note: there are 11 output files and I am interested in this one only
any other method to overcome such problem
I have presentation tomorrwo. hope things will work fine.
To: Toqa Manasrah
Subject: Re: [galaxy-dev] Urgent help needed
Sure. See the link in my previous email
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.