I am experiencing a few problems in configuring external tools.

ugene 1.9.2
on Windows

Application tested on cygwin to be working.

But I get:

[ERROR][18:02] Task {MAFFT validate task} finished with error: It is possible that the specified executable file for MAFFT tool is invalid. Tool does not start.
[ERROR][18:18] Task {T-Coffee validate task} finished with error: It is possible that the specified executable file for T-Coffee tool is invalid. Can not find expected message.
[ERROR][16:53] Task {FormatDB validate task} finished with error: It is possible that the specified executable file for FormatDB tool is invalid. Tool does not start.
[ERROR][16:53] Task {BlastAll validate task} finished with error: It is possible that the specified executable file for BlastAll tool is invalid. Tool does not start.

I am not sure what is wrong with it. Some how ugene cannot recognize/validate the programs...

[ERROR][09:58] Task {BlastN validate task} finished with error: It is possible that the specified executable file for BlastN tool is invalid. Tool does not start.
[ERROR][09:58] Task {BlastP validate task} finished with error: It is possible that the specified executable file for BlastP tool is invalid. Tool does not start.
[ERROR][09:58] Task {BlastX validate task} finished with error: It is possible that the specified executable file for BlastX tool is invalid. Tool does not start.
[ERROR][09:58] Task {MakeBLASTDB validate task} finished with error: It is possible that the specified executable file for MakeBLASTDB tool is invalid. Tool does not start.
[ERROR][09:58] Task {RPSBlast validate task} finished with error: It is possible that the specified executable file for RPSBlast tool is invalid. Tool does not start.
[ERROR][09:58] Task {TBlastN validate task} finished with error: It is possible that the specified executable file for TBlastN tool is invalid. Tool does not start.
[ERROR][09:58] Task {TBlastX validate task} finished with error: It is possible that the specified executable file for TBlastX tool is invalid. Tool does not start.
[ERROR][09:59] Task {T-Coffee validate task} finished with error: It is possible that the specified executable file for T-Coffee tool is invalid. Can not find expected message.

ok same here... not detected....
all 32bit..

Poh,
did you use external tools package that is provided on our web-site or did you download external tools by yourself?

I download it by myself? Is there a specific one that is needed?

For BLAST and BLAST+ it is resolved. It needed the blast-win32 or blast-win64 loaded in a path that does not have space. It worked.

However the blast output format is limited to Genbank? can't we have other formats say m8 (hit tables?) or other forms? I really need a hit table output so that I can put in a parser to filter the output first to remove the insignificant alignments.

Also the blast search interface needed to list the path and file for the formatted databases basenames so that users can identify the db files.

Clustalw done.

I still have problem with T-coffee, MAFFT. Any specific packages that I must go for?

was (apparently the raw output gb file from the blast result was not printed out? How could I transfer that result to other application to parse?)

ok... apparently when I save ugene that .gb file comes out. I would expect it to come out automatically when the blast process is running without the need for me to save it.

Check this webpage: http://ugene.unipro.ru/external.html
Our package contains pre-built MAFFT.

Prebuilt T-Coffee is not available for Windows. Details are here: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html

I will check issue with spaces in BLAST+ path and create bug if needed.

BTW,  did you check our public bug-tracker? You can register and contribute to project development by creating new issues for developers team.

Regarding BLAST output.

Use Workflow Designer capabilities to create custom analisys pipeline. For example in schema below (see screenshot), BLAST output is saved to gff, genbank or scv file with specified path.

Each schema can be used a command line tool with aliases for parameters. For instance you can alias output file name and launch your schema in any custom script like this:
ugene --task=path/schema.uwl --out=/path/out_file.gff

Check  for more details:
About Workflow Designer
Creating Schema
Running Schema from the Command Line

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ok, will move it to the public bug tracker...

I have just registered and have problem to login.
Will follow up on it.

Thanks!

Are you still facing these problems or it's running properly Poh?