Updating tools/cami_amber from version 2.0.4 to 2.0.5

[gxydevbot]

Hello! This is an automated update of the following tool: tools/cami_amber. I created this PR because I think the tool's main dependency is out of date, i.e. there is a newer version available through conda.

I have updated tools/cami_amber from version 2.0.4 to 2.0.5.

Project home page: https://github.com/CAMI-challenge/AMBER/releases

For any comments, queries or criticism about the bot, not related to the tool being updated in this PR, please create an issue here.

[bgruening]

@SantaMcCloud any idea why this fails with a python error?

[SantaMcCloud]

I will have a look on it

[SantaMcCloud]

It seems that the tool can not load the file correctly, or at least the path is not correctly split by the function. I will take a deeper look into it later and will create an issue, by cami amber, when I found out more @bgruening

[SantaMcCloud]

So I just review the code and push and open an RP CAMI-challenge/AMBER#56 and Issue CAMI-challenge/AMBER#57 to fix the problem. The problem was that they wrote new code but, I think, forgot about the genome_coverage file which also use the rewrote code and because of this it came to this problem.

[SantaMcCloud]

@bgruening They pushed a new version 2.0.6to fix the problem. So after updating it, it should work fine!

[bgruening]

Awesome, thanks for following up upstream.

I will wait for the conda bot to create a new package. Good that your tests catched this!

[SantaMcCloud]

No problem!

Yes, i try always to use all parameter in the test to catch any problem :)

[bgruening]

The bot is not doing it, can you create a new package?

[SantaMcCloud]

You mean Update the recipe or the wrapper?

[bgruening]

The recipe is missing correct?

[SantaMcCloud]

no it is not messing and the bot also update it to the current version https://github.com/bioconda/bioconda-recipes/blob/master/recipes/cami-amber/meta.yaml

[SantaMcCloud]

i can Manually edit the wrapper here to update it to 2.0.6or should i open a new PR?

[bgruening]

Ah ok, missed that update. Please update the file here in this PR. No new PR needed.

[SantaMcCloud]

How can I change it here since i don't have access to the branch? Via review?

[bgruening]

If you don't have write access you can use github suggestions: https://haacked.com/archive/2019/06/03/suggested-changes/

I just did this. If it turns green is it good to go from your side?

[SantaMcCloud]

Ah okay i did guess that it would work like this but befor i do something stupid i wanted to ask :)

Yes it is good for me when all test are positiv!

[SantaMcCloud]

And thank you!

[bgruening]

Thanks a lot for fixing this properly in upstream!