[Galaxy-Dev] Urgent Help Needed

Question: [Galaxy-Dev] Urgent Help Needed

7.0 years ago by

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, ________________________________________ 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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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modified 7.0 years ago • written 7.0 years ago by Toqa Manasrah • 70

7.0 years ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k wrote:

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

ADD COMMENT • link written 7.0 years ago by Dannon Baker ♦ 3.7k

7.0 years ago by

Toqa Manasrah • 70

Toqa Manasrah • 70 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, ________________________________________ 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

ADD COMMENT • link written 7.0 years ago by Toqa Manasrah • 70

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="${i nput1}reads_l_${parameter1}_${parameter2}_CNTGS_DIST0_EM20.txt" Good luck- Dannon

ADD REPLY • link written 7.0 years ago by Dannon Baker ♦ 3.7k

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