bioconda installable

[SilasK]

Hey @bastiaanvonmeijenfeldt

I' would make a bioconda installable of CAT. here
Could you give CAT a license?

Do you have any test to run?

If I'm not wrong you can make the CAT executable. This information is somehow stored even on github.

It would be great if you could update the version and sha256 when you have new releases.

[bastiaanvonmeijenfeldt]

Hi @SilasK,

Thanks for the feedback! All of your suggestions have been added to the to-do list, and will be included in future releases! I'll let you know if it's ready.

Best wishes,

Bastiaan

[SilasK]

Do you know which license you want to give CAT? In theory, I'm not allowed to use your code without a license.

[SilasK]

status: bioconda/bioconda-recipes#12536

[SilasK]

Yes It needs a license.
@bastiaanvonmeijenfeldt You can modify the recipe here

[bastiaanvonmeijenfeldt]

Hi Silas,

CAT will be available under CC BY 2.0. Thanks for your work on the bioconda recipe!

[SilasK]

It should bwork now!
conda install -c bioconda cat

[bastiaanvonmeijenfeldt]

It's not working for me yet:

Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - cat

Current channels:

  - https://conda.anaconda.org/bioconda/linux-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/linux-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/pro/linux-64
  - https://repo.anaconda.com/pkgs/pro/noarch

Also, I'm looking into the licenses and it will be CC BY 3.0.

[SilasK]

@bastiaanvonmeijenfeldt

I updated the version.
bioconda/bioconda-recipes#12587

You don’t have any preprint, do you?

It seems there is some latency on the bioconda side.

[bastiaanvonmeijenfeldt]

Great, thanks! There is a preprint but it's super old and CAT has changed a lot since then so not worth mentioning...

[SilasK]

@bastiaanvonmeijenfeldt Where are the releases gone? The bioconda package needs downloading it from the github. or any other stable url..

[bastiaanvonmeijenfeldt]

Yes sorry for that! We have moved stuff around since yesterday and in the process removed the released. A new one will come online shortly!

[bastiaanvonmeijenfeldt]

Hi @SilasK,

A new release is now online. CAT is executable so no need to chmod +x anymore. A license is added to the repository, as well as a changelog.

[SilasK]

@bastiaanvonmeijenfeldt

The cond build didn't worked because
psutil
is an additonal requeirement. I fixed it now. any other package to install?

[bastiaanvonmeijenfeldt]

Thanks for pointing this out to me! I've included psutil to get memory size but I don't want to have another dependency. All our other python imports are standard library. So I will remove the psutil import soon and fix this in another way...

List of packages CAT/BAT uses:

argparse
datetime
gzip
math
multiprocessing
os
psutil
subprocess
sys
tarfile
urllib.request

[SilasK]

For the condo package there is no need to drop plutil.

[bastiaanvonmeijenfeldt]

I have removed the psutil dependency with the latest release (4.3.1). I'd rather have a dependency less for people that are only running a bare version of Python.

[SilasK]

I could install CAT also on osx. Do you think it could work?

[bastiaanvonmeijenfeldt]

There is actually no reason it should not work, EXCEPT for the psutil-free memory check I just built in, haha. But this is not a big deal, I can make that work on mac OS as well, working on that now!

That being said, we have extensively tested CAT/BAT on Linux, and have not on mac OS, so no guarantees here. But I will build in mac compatibility and let's see what users think. :)

[bastiaanvonmeijenfeldt]

I have made CAT/BAT Mac OS compatible, the latest version is online.

@SilasK: I think it would be easiest if I update the sha256 and version in the Bioconda recipe every time I publish a new version, where can I do that? Is simply pushing the change enough or should there be versioning/tagging/releasing?

[SilasK]

Good Idea.

You are supposed to read the docs
In short:

• fork the bioconda repo
• Modify the cat recipe
• essentially change the tow first lines in the meta.yaml
• pull request
• wait until checks pass!
• merge

I'm not sure If you can merge the PR if you are not part of the biaconda association. But I can do it.

The last version is merged into the master branch, but there is always a short latency until it is available.

For versioning see here an example.

Later you can also add doi, and doc urls ...

Happy building!