maxquant: add dotnet-runtime requirement

[bernt-matthias]

When running maxquant I got:

.NET Core 3.1 needs to be installed. Please visit https://dotnet.microsoft.com/download/dotnet-core/3.1 and install the SDK x64.

TODO

• [ ] test this manually (within https://github.com/galaxyproteomics/tools-galaxyp/pull/716)

Describe your pull request here

---

Please read the guidelines for Bioconda recipes before opening a pull request (PR).

• If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
• New recipes not directly relevant to the biological sciences need to be submitted to the conda-forge channel instead of Bioconda.
• PRs require reviews prior to being merged. Once your PR is passing tests and ready to be merged, please issue the @BiocondaBot please add label command.
• Please post questions on Gitter or ping @bioconda/core in a comment.

Please use the following BiocondaBot commands:

Everyone has access to the following BiocondaBot commands, which can be given in a comment:

@BiocondaBot please update	Merge the master branch into a PR.
@BiocondaBot please add label	Add the please review & merge label.
@BiocondaBot please fetch artifacts	Post links to CI-built packages/containers. You can use this to test packages locally.

For members of the Bioconda project, the following command is also available:

@BiocondaBot please merge

Upload built packages/containers and merge a PR. Someone must approve a PR first! This reduces CI build time by reusing built artifacts.

Also, the bot watches for comments from non-members that include @bioconda/<team> and will automatically re-post them to notify the addressed <team>.

[bernt-matthias]

Does anyone know how we can get a working download link for maxquant? ping @veitveit @npinter @bgruening

Would be even better if the link would be stable...

[bgruening]

For this version I do not have a copy :( For older versions I do https://depot.galaxyproject.org/software/maxquant/

What about upgrading? But this will produce potentially a lot of downstream work.

[veitveit]

You generally need to provide your email address and name to download the software which makes it tricky to provide maxquant as a download link. Making it available through the link above looks like a good solution to me.

I had many problems when trying dotnet with Maxquant >=2.0 as there were always conflicts with either .NET core or dotnet itself. Maybe the newest versions solve that now.

[bernt-matthias]

I still asked: https://github.com/cox-labs/CoxLab_Bug_Reporting/issues/32

For the Galaxy tool it seems that dotnet 3.x seems to work https://github.com/galaxyproteomics/tools-galaxyp/pull/700/files#r1210918511

According to MQ docs dotnet >2.7 (linux) and >4.x (win) should work. but error message shows that at least 3.x is needed. So my suggestion would be to try something like >=3.1.

.. so probably its the best to bump the recipe here. For the Galaxy tool we can add the additional requirement there

[bernt-matthias]

The Changlog mentions: - Switch from .NET Core 2.1 to .NET Core 3.1 for 2.0.3.0

[veitveit]

Thanks a lot for taking care of this.

And good luck :-)!

[ovigy]

Hi, if it can help, please find unofficial repositories that contain old Perseus and MaxQuant versions.

• https://drive.google.com/drive/folders/1g-FdPFLaikosQMZQEQ9e3hqi0c4_WFV6
• https://drive.google.com/drive/folders/1Ja9iaCQ6mM66VQEeaS36hqq77bnsmxQF

Best regards, Oana

[bernt-matthias]

Cool :)

So my suggestion would be to mirror the currently available version in bioconda to depot.galaxyproject.org and add a note to the repository that this should be done as well for future versions.

I would also add a link to your archive which is an excellent resource.

[bernt-matthias]

@bgruening would a google drive link be fine? or should we create an independent backup?

[bgruening]

Let's use cargo-port.

[bernt-matthias]

OK https://github.com/galaxyproject/cargo-port/pull/172 .. just went for the newest version

• for the older we have a workaround
• and the checksums of the version in the google folder and the checksum here mismatches

[sorenwacker]

Could you add 2.3, and 2.4 ?