.NET Bio flashback

[filicado]

I have to revisit an old .NET bio project from a few years back. However, in the meantime I have left the Windows world behind. So I installed MonoDevelop (on Ubuntu 16.04) to see if it would work. I was trying to migrate the old code but it gives problems with simple things that worked fine. For example this:

    Sequence tsequence = new Sequence(Bio.Alphabets.RNA, line1.ToString());

Now throws an exceptions saying "The type initializer for 'Bio.Alphabets' threw an exception." Apparently I need to "add a reference to a Bio.Platform.Helpers library." Any ideas?

[markjulmar]

Just use the published Nuget package. It adds all the pieces you need for each platform.

On Tue, May 24, 2016 at 10:26 AM, filicado notifications@github.com wrote:

I have to revisit an old .NET bio project from a few years back. However, in the meantime I have left the Windows world behind. So I installed MonoDevelop (on Ubuntu 16.04) to see if it would work. I was trying to migrate the old code but it gives problems with simple things that worked fine. For example this:

Sequence tsequence = new Sequence(Bio.Alphabets.RNA, line1.ToString());

Now throws an exceptions saying "The type initializer for 'Bio.Alphabets' threw an exception." Apparently I need to "add a reference to a Bio.Platform.Helpers library." Any ideas?

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/dotnetbio/bio/issues/21

Mark Smith

mark@julmar.com | @marksm http://www.twitter.com/marksm | 214-774-4749 | www.julmar.com

[filicado]

This was actually my first attempt but that gave me: "Unable to resolve dependency 'NetBioCore.PCL (≥ 2.0.150722)'." For the references it says "Assembly not found for *"

• = no matter what I set the target to

[markjulmar]

Hmm.. that's weird. I wonder if MonoDevelop has issues with NuGet. The package is here: https://www.nuget.org/packages/NETBioCore.PCL/

I know Xamarin Studio (the Mac version of MonoDevelop) doesn't have any trouble. I'll ask Matt Ward who developed the plug in for the IDE.

But you can solve it easily enough by adding a reference (from source) to the proper platform-specific assembly. You want the full desktop variant. Or, check with Nigel, he's got a solution that combines it all into one DLL I think.

mark

On Tue, May 24, 2016 at 10:45 AM, filicado notifications@github.com wrote:

This was actually my first attempt but that gave me: "Unable to resolve dependency 'NetBioCore.PCL (≥ 2.0.150722)'."

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/dotnetbio/bio/issues/21#issuecomment-221314033

Mark Smith

mark@julmar.com | @marksm http://www.twitter.com/marksm | 214-774-4749 | www.julmar.com

[filicado]

That did the trick thanks, now only ~300 other issues to take care of

[evolvedmicrobe]

Dare I ask what the remaining 300 are? I run the library on Ubuntu all the time so have probably encountered some of them.

[filicado]

Sorry, nothing related to .NET bio I'm using it for pretty pedestrians stuff. It's just a small tool that generates TALEN coding sequences and makes sure that RVDs match each other as little as possible. Actually after I set the target to Mono 4.5 linq code also worked suddenly and it all ran (slow) fine!

[ambi1999]

HI Filicado,

How did you manage to solve this issue. I got similar message (on visual studio community 2015) recently and have not been able to resolve it.

Cheers, Ambi.