Make a bioconda package for metamorpheus

[acesnik]

We can use maxquant as an example: https://github.com/bioconda/bioconda-recipes/tree/master/recipes/maxquant

But first, we'll need dotnet to create a conda package like there is for mono dotnet/core#2518

[ypriverol]

Hi, do you have any progress here? Im interested to use a conda package

[trishorts]

I wish that we had. But, sadly no. We are really understaffed at the moment. I think this is something that would not take much time at all. But we haven't done this ever before as a group. So, there is no-one here with the knowledge. Building the knowledge is the thing that would take the most time I guess.

We would gladly take outside assistance.

[acesnik]

I might actually be willing to take this on in March. I want to learn python & conda packaging. By the way, dotnet-sdk is in conda-forge, now, so that issue is solved. https://anaconda.org/conda-forge/dotnet-sdk

[ypriverol]

I think should be bioconda. More than willing to help!!!

[ypriverol]

@trishorts @acesnik have you tested the tool on Mono 5.14.0.177?

[trishorts]

Anthony, i would be immensely grateful if you could find time to do this. And Yasset, if you'd be an alpha tester, that would really be helpful.

I don't know if mono would work or not. MM requires dotnet compatibility for every environment. I don't know if mono has that or not.

[bernt-matthias]

I also guess that conda-forge has the needed packages:

• dotnet
• dotnet-aspnetcore
• dotnet-runtime
• dotnet-sdk

These should be available in version 3.1 and 5.0

If you already have a script to compile from source a conda package at bioconda it might actually be easy to get this done ...

Feel free to ping me if you have questions.

[trishorts]

What a great offer. Thank you. This is something that I did not know.

[bernt-matthias]

Sure, https://anaconda.org/ offers a great way to search for packages. But I would not go beyond the conda-forge and bioconda channels.

[ypriverol]

We have a team here @bernt-matthias @trishorts. @bernt-matthias can you point us to a recipe of a dotnet bioconda package for @trishorts and me to see how it looks.

[bernt-matthias]

Seems that there is no package in bioconda yet that uses dotnet (so we could be the first .. I guess we will see some exciting problems LOL).

But we might start of with any package I guess.

Just take for instance https://github.com/bioconda/bioconda-recipes/blob/master/recipes/bamtools/. Essentially you need two files:

• meta.yaml: Contains all the needed metadata. The most important part is probably the requirements section. Where you list which software is needed for building and running the software. Specs are here https://docs.conda.io/projects/conda-build/en/latest/resources/define-metadata.html
• build.sh: A shell script that will build the package.

For a start you can create a PR at bioconda that: creates a folder in recipes containing these two files ... just adapt them to metamorpheus.

[acesnik]

Yes, the dotnet package in bioconda is pretty new, and it doesn't work on OSX yet, but I've made an issue for that on GitHub for the people who created that. 😄

Here's another example for MaxQuant, which is available in Bioconda https://github.com/bioconda/bioconda-recipes/tree/master/recipes/maxquant

[acesnik]

bioconda/bioconda-recipes#27130

[acesnik]

One thing to note is that bioconda doesn't support Windows builds. If anyone intends to use conda for fetching MetaMorpheus for the Windows commandline, we should consider sending the PR to conda-forge, which does do Windows builds.

[acesnik]

Adding this other issue here for reference #2036

[acesnik]

I tried making a PR to conda-forge (conda-forge/staged-recipes#14252) and ran into the same issues with the __glibc >= 2.17 requirement for using dotnet that I ran into with bioconda (bioconda/bioconda-recipes#27130).

I opened an issue on the dotnet-feedstock for conda-forge to ask for advice on how to proceed with this (conda-forge/dotnet-feedstock#16). Otherwise, I'm pretty stalled.

[acesnik]

I got some feedback from the developer of the dotnet conda-forge package:

[acesnik]

Hi all, I finished a PR to create a metamorpheus feedstock in conda-forge using dotnet that's awaiting review. conda-forge/staged-recipes#14252

[acesnik]

MetaMorpheus is now in conda-forge using dotnet. This makes it available on Windows, Linux, and macOS via conda.

MetaMorpheus PR:
#2050

PRs for the history of merging it into conda-forge:
conda-forge/staged-recipes#14252
conda-forge/staged-recipes#14623

Where to find it in conda-forge:
https://github.com/conda-forge/metamorpheus-feedstock
https://anaconda.org/conda-forge/metamorpheus

[bernt-matthias]

Hi @acesnik I just checked with a colleague who is using windows. I could not figure out how to run metamorpheus from the anaconda explorer or a command line with enabled environment. Do you have any tipps for us?

[acesnik]

Thanks for checking. I'm traveling this week, but I'll try to take a look.

Did conda install -c conda-forge metamorpheus work for installing it?

Were there any error messages? Running the command should be metamorpheus instead of dotnet CMD.dll, in case that's the issue.

[bernt-matthias]

@acesnik I installed via the anaconda GUI manager. I was also able to obtain a command prompt with activated environment, but unable to run the CLI, the binary / script was not found.

Btw. is it possible to run the GUI version from the conda package?

For linux everything worked fine.

[acesnik]

Good to know!

I'm currently traveling, so I'll be able to take a closer look in a couple weeks.

[acesnik]

It looks like this was an environment variable issue. I've fixed the Windows executable issue here: conda-forge/metamorpheus-feedstock#4.