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Problem creating .NET Bio Project v 1.01

Jul 4, 2012 at 4:12 AM

Greetings, folks, 

my sincere apologies if I'm not using the right communication channel, but I've just installed .NET Bio on top of VS2010 and when I try to create a C# .NET Bio project I get the error message:

"Error: this template attempted  to load component assembly 'Bio.TemplateWizard, Version=1.0.0.0..."...

Is this a known issue? My installation was successful, so I wonder if this dll shipped in package 1.0.1 and installed in the GAC is newer than what VS2010 expects to find.  Any help is much appreciated.

Thanks,

Jaumir.

Jul 4, 2012 at 1:57 PM

Hi Jaumir,

This is a fine place to post questions. I just checked and it should be looking for 1.01, not 1.00 so it's a problem with the installer.  I'll check in a fix shortly for it, however in the mean time an easy workaround is to use NuGet instead - it adds the same sample code to your project and I find it more usable than the template wizard since you can add the bio code to any project type - not just a console application.  If you aren't familiar with it, here's the basic process:

1) Install the NuGet extension (Tools | Extensions, search for NuGet, install).

2) Create an application - console application, WPF, etc.

3) Right click on the references node in the solution.

4) Select "Manage Nuget Packages"

5) Search for "biology" in the presented dialog - .NET Bio 1.01 should show up.  Click install.

Now you will have a new folder in the app with a "BioUtilities" static class that includes all the same helpers the template wizard generates for you - to load FastA, run an alignment, etc.

Thanks for reporting the version mismatch in the template wizard - it's a nice starting place so we certainly need to bump the version in the zip file.

mark

Jul 4, 2012 at 1:58 PM
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Jul 5, 2012 at 3:11 AM

Thanks for the help, Mark. Much appreciated.

Jaumir.

Sep 15, 2012 at 8:42 PM
Edited Sep 17, 2012 at 4:16 AM

I had the same error.

but in VS2010 when i click in Tools | Extensions i can't find NuGet

so,

1. I downloaded the Nutget in http://nuget.org/ and install it.

2. I created a console aplication.

3. Right click on the references node in the solution.

4. Select "Manage Nuget Packages"

5. Search for "biology" in the presented dialog - .NET Bio 1.01 should show up.  Click install.

i had everything ok, since this point, but i dont know what contains the template code. Is the BioUtilities.cs the same template code of the template?

I can't find the main method in BioUtilities.cs 

And this class contains the nexts methods:

AlignSequences

DoBEDMerge

DoDenovoAssembly

DoMultipleSequenceAlignment

DoSimpleSequenceAssemble

ExportFastA

ParseFastA

In the programming guide doesn't appears this methods.

Or otherwise anybody would help me with how to fix that just say in the Commit 75672?

 

where i found the path  bio/Source/Tools/Bio.TemplateWizard/BioConsoleApplicationTemplate/BioConsoleApplication.vstemplate,

in the source code or in the instalation path of .Net Bio?

I need help soon, greetings from manizales, colombia

 

 

Leonardo

Sep 19, 2012 at 6:01 PM

Hi Leonardo,

There is no main method - that's in your Console application already.  Instead, it adds the BioUtilities class which contains all the code from the template.  You work with it the same way you do the template - here's what the template generates basically:

static void Main()
{
   // TODO: call methods here 

You would do the same, just inside your Console application's Main method which should be in Program.cs. For example, to read a FastA file, you would call BioUtilities.ParseFastA passing a filename and it returns a list of sequences.  You can then pass that list of sequences to BioUtilities.AlignSequences, and then finally to BioUtilities.ExportFastA to push it back out to a file.

The original template worked the same way - it didn't write any code for you, it just had the methods there.  You were responsible for deciding what to use and the order to call the methods in.

I'll check on the template wizard too, although I prefer the Nuget approach because the template didn't work with Visual Studio Express which most academics tend to use since it's the free version.  (Express doesn't support custom project wizards).

mark

May 20, 2013 at 11:56 PM
After a long time, I retake this post, because, the programmer guide says:

"Visual Studio automatically displays the project’s program.cs file, which contains the template code."

When you create, an Console Aplication, and add the .NET Bio references via NUTGET, you dont have the template code like say in the Programming guide.


Regards,

Leo
May 21, 2013 at 3:20 PM
Correct. The documentation was written before we started the NuGet distribution option. The documentation only refers to creating a project using the .NET Bio project template. When you use Nuget, you get a set of helper classes which include all the same code but no Program.cs or Main method since you already would have that (Nuget can only be used AFTER you create a project, so your current project would have the entry point already defined).

mark
Dec 30, 2013 at 1:16 PM
I upgraded from version 1.01 to 1.1 on Nov. 14, 2013 and when I try to use the project template, I get the same error message as Jaumir:

'Error: this template attempted to load component assembly 'Bio.TemplateWizard, Version=1.0.0.0...'

Is this a matter of the project template installer not yet being fixed or has the project template been removed from 1.1 and I am left with a relic of a project template from version 1.01?

I found this thread and have done the NuGet thing, although that has not gotten me any farther than I already was, as I had previously figured out how to add references to the dll's that were in the folder for the installation of .Net Bio.

The point of this posting is that the documentation seems to be out of sync with the software, as it still refers to the project template (which did not work for me) and does not mention NuGet.

I have lost numerous hours trying to work through this and it has not gotten me any further towards the issue I was trying to resolve (I will post that separately if a different path does not solve it).

I suspect many potential contributors to .Net Bio would have just given up by now. I greatly appreciate the idea of .Net Bio and the effort that has gone into it, but I suspect the relative lack of contributions and use are due to rough edges like this.
Dec 30, 2013 at 3:01 PM
Hi,

Yes, 1.01 is still there -- 1.1 is not an upgrade, it's a separate release. You have to uninstall 1.01. However, that said, don't bother with the project template. Instead, do this:

1. Create a Console Application (or WinForms, or WPF, or any other .NET application type you want to create).

2. Right click on References and select "Manage Nuget Packages"
3. Select the Online choice and in the search box, type ".NET Bio".
4. Click "Add".

This will add the same code the template originally did and is the preferred mechanism to getting the latest .NET Bio installed as Nuget will auto-update and can be installed into any application type (the project template only allowed for console apps).

If you need more explicit instructions, please let me know - I'd be happy to send screen shots. Have a great New Year!

mark



Dec 30, 2013 at 5:26 PM
Hi RMarkT,

Thanks for using .NET Bio - and I agree with you that a bioinformatics library using the .NET framework has real potential - like many open source projects though, it relies on the dedication of volunteers - and with a large codebase dealing with a technical subject, this takes considerable effort. Unfortunately while we have a reasonable community using the project, volunteers to help out are rarer.

Some of the issues you mention are likely to get fixed - but naturally enough, most volunteers are only interested in fixing issues that affect them. If you had some time, the issues you mention would be a great place to start. Did you create this as a bug/feature request? If you look under 'Issues' in the menu bar you will find out how. Also, if you would like to help us out just assign some of these issues to yourself and we'd be happy to have you as a contributor.

Happy Christmas,

Simon
Jan 6, 2014 at 12:37 PM
Hi RMarkT
Let me echo Simon's welcome and encourage you to post further, especially if you want to contribute and if you would like to tell us a bit more about the application. There is a bit of a backlog of things to be updated and uploaded following on from the holidays, but most people are returning to work and will welcome further thoughts and contributions.
All the best,
jh