UGENE Forum - Multiplexer

Mar 19^th, 2012 at 8:52am

kenkl Offline
Junior Member

Posts: 73

Hi there,

I'm trying out on the function of the multiplexer for my workflow. Is it possible that I could parse the information from the multiplexer into 1 single element? I had tried it but it would not work, I'm trying to parse the information into LUCY trimmer which requires 2 input data from 2 upstream element, 1 FASTA file and 1 quality file.

When I tried the multiplexer the other way, that's by parsing it out to 2 "Write" elements, it worked seamlessly.

Kindly advice on this.

P/S: I had attached the screenshots for your reference. 1 is the successful one with 2 out elements, and 1 is the one that crashes with 1 out element.

success.png (139 KB | )

crash.png (157 KB | )

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Reply #1 - Mar 20^th, 2012 at 9:31am

German Offline
Full Member

Posts: 118

kenkl wrote on Mar 19^th, 2012 at 8:52am:

Hi there,

I'm trying out on the function of the multiplexer for my workflow. Is it possible that I could parse the information from the multiplexer into 1 single element? I had tried it but it would not work, I'm trying to parse the information into LUCY trimmer which requires 2 input data from 2 upstream element, 1 FASTA file and 1 quality file.

When I tried the multiplexer the other way, that's by parsing it out to 2 "Write" elements, it worked seamlessly.

Kindly advice on this.

P/S: I had attached the screenshots for your reference. 1 is the successful one with 2 out elements, and 1 is the one that crashes with 1 out element.

Kenneth, which multiplexing rule do you set for the multiplexer?

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Reply #2 - Mar 20^th, 2012 at 9:50am

kenkl Offline
Junior Member

Posts: 73

Hi!

I used 1 to 1 rule.

Thanks!

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Reply #3 - Apr 5^th, 2012 at 11:36am

German Offline
Full Member

Posts: 118

Kenneth, the issue has been resolved (https://ugene.unipro.ru/tracker/browse/UGENE-908).
There was our internal mistake. Thank for your bug report!

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Reply #4 - Apr 5^th, 2012 at 2:17pm

kenkl Offline
Junior Member

Posts: 73

Wow, that's great news! Waiting eagerly for the snapshot release now!

Thanks!!

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Reply #5 - Apr 5^th, 2012 at 5:55pm

German Offline
Full Member

Posts: 118

I have tried to use lucy from UGENE WD. It works well. You can see the scheme on the attached screenshot.

I have added a new output slot type "Output file url" for external tools workers. It is the analog of "Read as String value".

When the external tool worker finished its running process then the file, corresponding with the "Output file url" slot, is not deleted. And this url could be used in next scheme elements.

But the file will be deleted after finishing the workflow. So, your wishes, that described here (https://ugene.unipro.ru/tracker/browse/UGENE-896), are not satisfied. But this issue will be resolved asap.

lucy.JPG (73 KB | )

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Reply #6 - Apr 6^th, 2012 at 2:33pm

kenkl Offline
Junior Member

Posts: 73

Hi German, do you mind sharing what are the parameters that you've set for LUCY?

Does the LUCY gives any output?

Thanks!

Kenneth

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Reply #7 - Apr 10^th, 2012 at 1:56pm

German Offline
Full Member

Posts: 118

kenkl wrote on Apr 6^th, 2012 at 2:33pm:

Hi German, do you mind sharing what are the parameters that you've set for LUCY?

Does the LUCY gives any output?

Thanks!

Kenneth

Here is my execution string:

lucy -v $first_file $second_file $seq_url $qual_url -output $good_seq $good_qual_url

$first_file - url parameter (PUC19);
$qual_url - url parameter (PUC19splice);

$seq_url - input "Read as string value" text port (it is fasta files from ttuner_seq);
$qual_url - input "Read as string value" text port (it is qul files from ttuner_quality);

$good_seq - output fasta sequence slot;
$good_qual_url - output "Write as output file url" text slot (qul files from lucy);

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Reply #8 - Apr 10^th, 2012 at 4:10pm

kenkl Offline
Junior Member

Posts: 73

Hi,

I'm facing problem with LUCY, it works well before hand and not sure why it does not work now. Had troubleshoot it with possible faults but still can't work.

I set the same parameters as yours, I could still run LUCY on command line, and it still runs when I hardcode the path to input data files.

Need help on this. Thanks!

Kenneth

« Last Edit: Apr 12^th, 2012 at 7:45am by kenkl »

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Reply #9 - Apr 11^th, 2012 at 9:56am

German Offline
Full Member

Posts: 118

Kenneth,
as I can see from the screenshot, your lucy element works well, because "File list" has produced only one message and lucy has retrieved it (0 in queue, 1 passed).
So why do you think that the problem is in lucy element?

I have seen your post about AWK scripts but I haven't investigated the problem yet.

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Reply #10 - Apr 12^th, 2012 at 7:45am

kenkl Offline
Junior Member

Posts: 73

Hi German,

Sorry, I had attached the wrong screenshot for your reference. This is the one that I'm supposed to attach. I'm unsure of what went wrong as apparent lucy just doesn't work in UGENE, the execution string are the same as previous and it works previously but not sure why. Please help on this yea, thanks!

Kenneth

lucy_fail.png (62 KB | )

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Reply #11 - Jul 2^nd, 2012 at 12:26pm

Octavio Igtanloc Offline
YaBB Newbies

Posts: 1

kenkl wrote on Apr 5^th, 2012 at 2:17pm:

Wow, that's great news! Waiting eagerly for the snapshot release now!

Thanks!!

Thank you,very much! Kiss

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