Dear Sir,

Ops, thanks for correct me.
Erm... After try it again and its still giving the same error saying "Error opening URL for read:" 

I have tried this task on Ubuntu with the last snaphot of UGENE (that you have too).

How have I created the new element? You can see it in attachments.
I haven't set environment variable for "ttuner", so I have typed the full path to "ttuner".
Maybe you should do it too?

Then I created a schema and run it.

PEH wrote on Jan 31^st, 2012 at 3:23pm:


It is very good that we finally found a decision! Congratulations!

Sorry, but I didn't understand clear your last question.

Yes, UGENE provides setting up parameters when you are creating a cmdline element. I have already wrote about it:
http://ugene.unipro.ru/forum/YaBB.pl?num=1326766085/0#6

Maybe those problem was because you set incorrect URL to the created "fof" parameter?

By the way, this mechanism (creating external CMDLine workers) provides running some external programs from UGENE and we have no any way for controlling and retrieving errors from these programs.

I think, TraceTuner prints something into stdout about its problems when you launch your broken example, but we can not catch these messages. UGENE just runs ttuner and waits while the last one is finished up.

Thanks for your feedback. It is very necessary for us to get error reports from users

PEH wrote on Jan 31^st, 2012 at 5:54pm:


This schema is not so good.
First of all, ABI files are not just for keeping sequences. They keep sequences and chromatograms. As you can see from the Workflow Designer manual, UGENE Wokrflow Designer has 4 datatypes: Sequence, Annotation, MSA, String.
So, when you read an ABI file by the "Read sequence" element, its output port has no any chromatogram, it contains just a sequence from the file.

You set the "infile" parameter format as "FASTA". So, what is happening in UGENE?
1) The "Read sequence" element reads a sequence from your ABI files and sends it to "abi2fasta". The "infile" parameter format is FASTA, so the sequence is saved into tmp file with FASTA format.
2) abi2fasta runs ttuner:
./ttuner created_tmp_file.fa -sa another_tmp_file.fa
because of the "outfile" parameter format is also FASTA.

So, you can see that "./ttuner created_tmp_file.fa -sa another_tmp_file.fa" is not good execution string. You can run simple ttuner with such way and you would see that it will be not working.

-----------------

You should understand, that when you create input/output port with Sequence type and with name "qqqqq", and if you write execution string:
"<your_tool> $qqqqq"
then the real execution string will be:
"<your_tool> temporary_file.<chosen_format>"

Dear Sir,

I'm facing the same stated problem regarding the integration of ttuner into the WD using CMD line elements. I'm using the latest UGENE 1.10.2 and its still not working. Kindly advice.

Regards,
Kenneth

Yes.

I could reproduce the one you had posted earlier in the post, however when I set URL as a parameter to browse for my own input data it failed with an error of "error opening URL to read" and then a statement stating "nothing to write:no document".

I had the snapshots of what I had been doing but could not upload it on my post since yesterday.

Hope you can help. =)

Regards,
Kenneth