UGENE Forum - Newbie: Facing problem on CMD Tools

May 4^th, 2024 at 12:54pm

Choose Language:

	Welcome, Guest. Please Login or Register
	Welcome to our forum.

UGENE Forum › General Category › Help and How-to › Newbie: Facing problem on CMD Tools

‹ Previous Topic | Next Topic ›

Pages: 1 2 3 4 5

Print

Newbie: Facing problem on CMD Tools (Read 78256 times)

Reply #45 - Feb 16^th, 2012 at 3:34pm

kenkl Offline
Junior Member

Posts: 73

Yes, appreciate that very much!

Besides, there is another issue too regarding ttuner. I had to hardcode path to fof.txt containing abi files in order for the elements to work, and when I change the path to input from read sequence it does not work. Thus can I request an element such as "Read ABI" to be included in 1.11 or that abi file to be supported in the input sequence. THanks!

Kenneth

IP Logged

Reply #46 - Feb 16^th, 2012 at 4:20pm

German Offline
Full Member

Posts: 118

kenkl wrote on Feb 16^th, 2012 at 3:34pm:

Yes, appreciate that very much!

Besides, there is another issue too regarding ttuner. I had to hardcode path to fof.txt containing abi files in order for the elements to work, and when I change the path to input from read sequence it does not work. Thus can I request an element such as "Read ABI" to be included in 1.11 or that abi file to be supported in the input sequence. THanks!

Kenneth

This issue could be resolved using a new element "Get files". See:
https://ugene.unipro.ru/tracker/browse/UGENE-817

You can set the input directory for this element and set include or exclude filters for filenames.
This element has only one output slot (url slot). It produces paths to files in the specified directory.

Another useful improvement is a new type for input slot of custom elements ("String value"). See:
https://ugene.unipro.ru/tracker/browse/UGENE-819

You can set up your custom "ttuner" element using a way that the input is not a sequence, but it is a string value. See the first screeshot.

And this string value would not be saved to the temporary file (like it is made for all other types). This string value would be placed directly to the execution string instead of $in. So, your ttuner execution string would be:
ttuner -sa $out $in

And your scheme would be like the scheme on the second screeshot.

These improvements will be available in the 1.11 version.

string_value.JPG (49 KB | )

scheme.JPG (22 KB | )

IP Logged

Reply #47 - Feb 16^th, 2012 at 4:49pm

kenkl Offline
Junior Member

Posts: 73

Great to hear that! Are these features available in snapshots? Thank you very much!

IP Logged

Reply #48 - Feb 16^th, 2012 at 4:56pm

German Offline
Full Member

Posts: 118

kenkl wrote on Feb 16^th, 2012 at 4:49pm:

Great to hear that! Are these features available in snapshots? Thank you very much!

Yes, they will be available in snapshots in several hours or tomorrow. Now, these snapshots are being built.

IP Logged

Reply #49 - Feb 16^th, 2012 at 5:02pm

kenkl Offline
Junior Member

Posts: 73

Ok, thanks!

IP Logged

Reply #50 - Feb 17^th, 2012 at 10:41am

kenkl Offline
Junior Member

Posts: 73

Hi there! I had downloaded the latest snapshot for Linux Distribution installed as 1.11-dev. There are several flaws that I had noted, error prompt in log when launched in 1.11-dev, but the other major problem is that the custom CMDline element that worked well in 1.10.2 now can't work at all in 1.11-dev. Please see screenshot. Kindly advice, thanks!

success_ugene1_10_2.png (166 KB | )

error_1_11-dev.png (170 KB | )

ugene_error.png (53 KB | )

IP Logged

Reply #51 - Feb 17^th, 2012 at 10:44am

kenkl Offline
Junior Member

Posts: 73

Besides, its good to know that in WD, workflow designed using earlier versions are not compatible to later versions. Can this issue be fixed as it would be very problematic for users that relies on custom CMDline element to re-create the element again in latest version. Thanks!

IP Logged

Reply #52 - Feb 17^th, 2012 at 11:03am

German Offline
Full Member

Posts: 118

kenkl wrote on Feb 17^th, 2012 at 10:44am:

Besides, its good to know that in WD, workflow designed using earlier versions are not compatible to later versions. Can this issue be fixed as it would be very problematic for users that relies on custom CMDline element to re-create the element again in latest version. Thanks!

Workflow schemes are compatible with earlier versions.

As I can see from the screenshots your workflow doesn't work because of config file problems. Try to delete the old config file (of the 1.10.2 version):

~/.config/Unipro/UGENE.ini

IP Logged

Reply #53 - Feb 17^th, 2012 at 11:32am

kenkl Offline
Junior Member

Posts: 73

Thanks! Its working well now. But its good to note that when I launch the snapshot it displayed error in log, which is not apparent in 1.10.2, see screenshot. Besides I cannot find this fixed feature in 1.11-dev:

https://ugene.unipro.ru/tracker/browse/UGENE-819

Thanks!

Kenneth

ugene1_10_2.png (33 KB | )

ugene_error_001.png (53 KB | )

IP Logged

Reply #54 - Feb 17^th, 2012 at 11:47am

German Offline
Full Member

Posts: 118

kenkl wrote on Feb 17^th, 2012 at 11:32am:

Thanks! Its working well now. But its good to note that when I launch the snapshot it displayed error in log, which is not apparent in 1.10.2, see screenshot. Besides I cannot find this fixed feature in 1.11-dev:

https://ugene.unipro.ru/tracker/browse/UGENE-819

Thanks!

Kenneth

Do you use "Linux binary package, i386 (32 bit)" or "Linux binary package, x86-64 (64 bit)"?
If you use the 32 bit version then try to download it again, please, because this version was not built yesterday but it is available now:
http://ugene.unipro.ru/downloads/unstable/ugene-1.11.0-dev-linux-i686-r1554.tar....

But if you use 64 bit version, this feature should be available there. Are you sure that you have chosen the "String" type for the slot? (See the screenshot).

string_value_001.JPG (49 KB | )

IP Logged

Reply #55 - Feb 20^th, 2012 at 9:16am

kenkl Offline
Junior Member

Posts: 73

Thanks Sir, no issue with that anymore as it is now working well.

Now I'm trying to write my output data in either .tab / .XML format but finds that the Write Plain Text does not support tabulated format. Any idea on that? Or can come up with an element that can probably function like the "String Value" created? Output the file as it is.

Thanks!

Kenneth

IP Logged

Reply #56 - Feb 20^th, 2012 at 9:30am

kenkl Offline
Junior Member

Posts: 73

Sorry for bothering again. I'm also trying to incorporate several other tools, one of such is MISA or namely Microsattelite Identification Tool. This tool uses totally different file type in its pipeline, made of 4 components which I had to separate them into components.

The problem arises as these components each receive and output different files:
misa.pl (input .fa) (output .fa.misa)
p3_in.pl (input .fa.misa) (output .p3in)
primer3 (input .fa.p3in) (output .p3out)
p3_out.pl (input .p3out) (otuput .result)

I could foresee that the WD might not be able to support such file types, could anything be done on it? Perhaps also include the "String Value" on Output slot as well?

Thanks!

IP Logged

Reply #57 - Feb 20^th, 2012 at 1:58pm

German Offline
Full Member

Posts: 118

kenkl wrote on Feb 20^th, 2012 at 9:30am:

Sorry for bothering again. I'm also trying to incorporate several other tools, one of such is MISA or namely Microsattelite Identification Tool. This tool uses totally different file type in its pipeline, made of 4 components which I had to separate them into components.

The problem arises as these components each receive and output different files:
misa.pl (input .fa) (output .fa.misa)
p3_in.pl (input .fa.misa) (output .p3in)
primer3 (input .fa.p3in) (output .p3out)
p3_out.pl (input .p3out) (otuput .result)

I could foresee that the WD might not be able to support such file types, could anything be done on it? Perhaps also include the "String Value" on Output slot as well?

Thanks!

Yes, if we support the "String value" format for the output data of custom elements then users could create their elements with arbitrary input/output file formats. The corresponded issue is created:
https://ugene.unipro.ru/tracker/browse/UGENE-847
We will resolve it asap.

Thanks for your ideas, Kenneth!

IP Logged

Reply #58 - Feb 20^th, 2012 at 4:40pm

kenkl Offline
Junior Member

Posts: 73

No problem, thanks for such a great effort in putting UGENE together! Anyway, will this new feature be included in 1.10.3/1.11?

Thanks

Kenneth

IP Logged

Reply #59 - Feb 21^st, 2012 at 9:52am

German Offline
Full Member

Posts: 118

kenkl wrote on Feb 20^th, 2012 at 4:40pm:

No problem, thanks for such a great effort in putting UGENE together! Anyway, will this new feature be included in 1.10.3/1.11?

Thanks

Kenneth

Yes, we will try to implement them for the 1.11 version.

IP Logged

Pages: 1 2 3 4 5

Print

‹ Previous Topic | Next Topic ›

Top of this page

UGENE Forum » Powered by YaBB 2.5 AE!
YaBB Forum Software © 2000-2010. All Rights Reserved.

Valid XHTML

Valid CSS

Powered by Perl

Source Forge