Hi,

If I understand your setup correctly, you have taken the original clustalw, ncbiblast, etc. perl code and put it directly into your new directory. And then you created a new Galaxy XML file which calls the appropriate Perl script in that same directory. This is totally fine in theory, but you need to make sure that the inputs and outputs are being handled correctly. I think your problem may be that you never give the the Perl script the name of the output files you want the tool to produce in Galaxy. You also need to give it the input file name. The way Galaxy handles inputs and outputs is by name--when you specify an output variable in the XML, Galaxy creates a file on the file system, which is associated with the output variable name in the XML. It is generally incorrect behavior if your tool generates a file that it names itself, without it being one of the output files already created by Galaxy. So if the Perl script does not accept inputs or outputs as arguments, you should modify it to do so. You also need to make certain that the command you have near the top of the XML file has all of required arguments for the Perl script (either hard-coded or based on parameters in the XML file), in addition to the named inputs and outputs.

If this doesn't help you get it working, send us one of your XML files and the Perl file associated with it and we can take a look.

Regards,
Kelly


On 4/2/10 10:42 AM, aeman zahra wrote:
I am a student of Bs Bioinformatics. I have been using the open source galaxy platform to integrate tool and make a work flow as my Final semester project. My supervisor happens to be ill and thus is unable to facilitate me in any respect. I here by take this opportunity to request that If any of you could help me fixing my problem. I would extremely grateful.
PROBLEM
My project problem is that , first of all i am using perl code tools for galaxy because galaxy dose not support installed tools from command prompt. so m using perl code tools for example clustalw, wublast, muscle and many more. sir these perl code tools are running correctly on command prompt and give me desire output, but when i put them it to the galaxy by making there xml file it gives an error that error occour while running this job.. and sir actually galaxy took tool's correct output as an error. i dnt know how to resolve it i tried alot but couldnt resolve it..
sir breifly m telling you that how m embedding perl code tools into galaxy:
1.go to ebi site, there are some perl code tools like clustalw, muscle,ncbiblast etc
2.i took them and download them
3. go to command prompt and try to run them by giving commands like
   perl ncbiblast.pl -S aemanzahra@comsats.edu.pk -D uniprot -P blastp
4.when it runs correctly i put them and embed them into the galaxy.
now in galaxy
1. insatlled galaxy
2. go in to tools directory
3. make a new directory of new tool ito tools directory e.g clustalw tool
4.go into clustalw tool and made two files in it. clustalw.pl in which perl code of clustalw tool is present.
   and secondly clustalw.xml is present of this tool that i made.
5.then run galaxy by sh run.sh command
6.galaxy web page opens
7. and i clicked on my added tool clustalw there and give it an input file of multiple sequences.
8. it runs. but after running it gives me an error that "error occour while running this job" but it took the output files of this tool as an error.
"The tools  run and three output files are created but the Galaxy takes them as errors."
WHAT PROBLEM IS THERE?
 
waitin for your reply
regards aeman


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