Tcode (and other emboss programs)

usegalaxy.eu support
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1

Hi, today most EMBOSS web GUI servers are down (i.e. EMBOSS explorer), however GALAXY implements most of the EMBOSS programs., but the graphic output is disabled, so programs like tcode or syco (and many others) can not be used. The EMBOSS version installed at GALAXY is 5.0.0 however it is available 6.6.0. The graphic output fails because png files are not a recognized format by GALAXY.
it would be nice to activate graphics output and update the version.
Thanks

2

Welcome, @H1889 !!

Great question! I agree that it would be nice to have these updated. And, incorporating png graphics as an output shouldn’t be a problem anymore.

So – since Galaxy is a community project, we rely on community developer contributions for most of the dev work. One way to learn about the status for tools is to review the development repository, or as in this case, the entire tool suite

  1. Load up the tool form in a Galaxy session
  2. Use the Options menu in the upper right corner → See in ToolShed
  3. Navigate using the Development Repository link

For EMBOSS v 5, that points to here tools-iuc/tools/emboss_5 at main ¡ galaxyproject/tools-iuc ¡ GitHub. I see several tickets already created about an update to v 6 plus other related items. This is good news since it means others are already interested in this project!

If you are also interested in working on this, you can comment on one of the tickets, or reach out to the IUC directly. Even if you are not interested in doing the technical development work itself, having another scientific contact is valuable! Maybe you can help to make the usage between different platforms more consistent? To better handle use cases like the one you describe, and maybe others that come up later.

I’m glad you asked about this, since posting here gets more eyes on it! This seems like a great project for someone out in the wild looking for a project that will be challenging and has public visibility, but is still within defined/clear bounds.

Thanks! :hammer_and_wrench:

3

Thanks for yout help. I posted this issue as a user I do not understand how works GALAXY, so I doubt that I can be of any help,.at most I would serve for testing purposes
Who can I talk to to help me solve the EMBOSS problems in GALAXY?
I have post this same issue at the Galaxy Training network (https://app.gitter.im/#/room/#Galaxy-Training-Network_Lobby:gitter.im) and a user (bgruening) is helping me.
I’m sorry I’m not very clear but I don’t know very well how galaxy works from an administrative point of view and I don’t know who I should contact to correct errors.
Thanks and greetings

4

Hi @H1889

Great that you are talking with @bjoern.gruening! He is the lead administrator for the EU server, and one of the people that can help to organize tool updates.

For tool errors themselves, you can ask questions here at this forum, or at the GTN chat. :slight_smile: We will need details, and this topic in the banner explains how to provide those → How to get faster help with your question

Specifically, you can share your history and explain what is going wrong, or you can screenshot or copy/paste all of the job details and logs. Sharing a history is easier, especially if you are new to Galaxy, and leads to faster and better solutions but what to do is your choice.

5

Thank you for the help. Here is my history:

as you can see the emboss programs syco and dotmatcher generate a graphic output in png format, however those files have 0 bytes.
Greetings

6

Hi @H1889

Yes, I can confirm that the empty outputs you are getting are related to the png file format not being supported at the public Galaxy servers for now. “Not supported” means that the files can be empty (same as your result).

There is nothing that can be done from the end user side to resolve the technical issue – the developers will need to resolve this, and it sounds like they know what is going on.

Hopefully this will be resolved soon! :hammer_and_wrench:

7

Thanks.
Greetings

8

A year ago, I placed a similar issue. Please import history MASTER_TEMA_2 and visualize syco or dotmathcer graphic output. The image is not generated.

I would really appreciate it if you could resolve this.

Thanks

1 Like
9

Hi @H1889

Yes, this project is still waiting for a developer to have time to work on the update. This is a large project for technical reasons. I see your additional ticket, too. The whole suite goes together and would get the version update changes.

For anyone else reading, this is the newer ticket

And is included in this search now too.

And this is the working PR

Maybe the developer can comment more about the status and plans. Hi @bernt-matthias do you have anything to add? Thanks!!

10

thanks for the information. I have remembered a FAQ at the original EMBOSS sourceforge page that, perhaps, could help you to resolve the problem:

Q) What Graphics options are available?

A) To see what graphics drivers are available type ? at the promt for the graph type and this will give you a list.

Here are some of those:-

   ps      -> Postscript
   cps     -> Colour Postscript
   x11     -> X display. (also called xterm and xwindows)
   hpgl    -> HP Laserjet III, HPGL emulation mode.
   png     -> PNG (you will need png, z and gd libraries for this)
   tek     -> Tektronix Terminal
   none    -> None.
   data    -> Writes out points to a file for graphs.
   meta    -> plplot meta file.

Are the png, z and gd libraires installes at your usegalaxy servers?

And please read this entry of de EMBOSS admin requirements:

“Graphics Requirements

Depending on your system you may need to explicitly configure the graphics. EMBOSS includes the plplot graphics library and will link to X11 and the recent (non-GIF) releases of the gd graphics library which also require libz and libpng (and possibly libjpeg). Please see the section ‘Configuring EMBOSS graphics’ below.

To get PLPLOT to produce PNG images you will need to have the

z

png

gd

gd

version$>=$1.8.4 is recommended. A recent release must be used as older versions support GIF which is NOT supported in later versions because of software patent problems. If for some reason you do not have the required libraries and your system support group will not update them for the system then install all three latest versions (

z

,

gd

,

png

) to a new directory and then add this new directory to your configure line forEMBOSS–./configure --with-pngdriver=my_dirwhere the

z

,

png

and

gd

libraries were each installed using./configure --prefix=my_dir

??? It may also be helpful to ensure that the

LD_LIBRARY_PATH

environment variable is set appropriately to include the libraries in the path. ???

These also list the various mirror sites for non UK people.

Alternatively, using ftp :-

You can unpack the tar.gz files in any directory, and install them in a common area.

By default everything (including EMBOSS) installs in /usr/local but in the examples below we use /home/joe/local

Note: gd does not use a ./configure script, and will fail at the “make install” stage if the installation directory does not have a /bin subdirectory. You can create this directory (e.g. /home/joe/local/bin) if it does not already exist.”

best regards