Adding to Bioconda

[rpetit3]

Hi @bede

Hostile looks pretty awesome! You've pretty much got everything already in place to submit to Bioconda.

Are you OK if I do this? Otherwise if you are planning to, I'll hold off.

Cheers! Robert

[bede]

Hey @rpetit3 and thanks for the issue! Haha this is on my todo list this afternoon. I'll give it a try now and assuming I don't have trouble, perhaps you could approve my PR as I recall you are a bioconda maintainer?

[rpetit3]

Yep! Just request me as a reviewer. I'll go ahead and close this

[bede]

Thanks, that was a good refresher for me on how to make a recipe and A LOT easier than packaging readItAndKeep!

[bede]

Thanks for all of your help with the recipe @rpetit3. I'm having issues which might relate to bowtie2's requirements for Python <3.11.0? Do you think unpinning tqdm's version here could help?

(base) ubuntu@pikachu:/data/bench2$ mamba create -n hostile -c bioconda hostile

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (1.4.4) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

Looking for: ['hostile']

bioconda/linux-64                                           Using cache
bioconda/noarch                                             Using cache
conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
pkgs/main/noarch                                              No change                                                                                                                                    
pkgs/r/linux-64                                               No change                                                                                                                                    
pkgs/r/noarch                                                 No change                                                                                                                                    
pkgs/main/linux-64                                            No change                                                                                                                                    
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
Could not solve for environment specs
The following package could not be installed
└─ hostile   is uninstallable because it requires
   └─ tqdm >=4.65.0 , which conflicts with any installable versions previously reported.

[mbhall88]

Weird, if I run the exact same command it creates the environment and installs fine...

Bowtie2 doesn't seem to pin a python version? https://github.com/bioconda/bioconda-recipes/blob/master/recipes/bowtie2/meta.yaml

Not sure what's happening here. @rpetit3 is the conda ninja though so hopefully he can get to the bottom of it

[rpetit3]

I also cannot replicate on my end

mamba create -n hostile -c conda-forge -c bioconda hostile
....
Looking for: ['hostile']

bioconda/noarch                                      4.5MB @   3.8MB/s  1.3s
pkgs/r/noarch                                                 No change
pkgs/main/linux-64                                   5.9MB @   4.2MB/s  1.5s
pkgs/r/linux-64                                               No change
bioconda/linux-64                                    5.1MB @   3.2MB/s  1.6s
pkgs/main/noarch                                   851.4kB @ 501.2kB/s  0.3s
conda-forge/noarch                                  13.3MB @   2.6MB/s  5.3s
conda-forge/linux-64                                33.0MB @   4.6MB/s  7.6s
Transaction

  Prefix: /home/robert_petit/miniconda3/envs/hostile

  Updating specs:

   - hostile

  Package                        Version  Build               Channel                    Size
───────────────────────────────────────────────────────────────────────────────────────────────
  Install:
───────────────────────────────────────────────────────────────────────────────────────────────

  + _libgcc_mutex                    0.1  conda_forge         conda-forge/linux-64     Cached
  + _openmp_mutex                    4.5  2_gnu               conda-forge/linux-64     Cached
  + anyio                          3.7.1  pyhd8ed1ab_0        conda-forge/noarch         97kB
  + bowtie2                        2.5.1  py310ha0a81b8_2     bioconda/linux-64          15MB
....
  + tqdm                          4.65.0  pyhd8ed1ab_1        conda-forge/noarch       Cached
  + typing-extensions              4.7.1  hd8ed1ab_0          conda-forge/noarch       Cached
  + typing_extensions              4.7.1  pyha770c72_0        conda-forge/noarch       Cached
  + typing_inspect                 0.9.0  pyhd8ed1ab_0        conda-forge/noarch         15kB
  + tzdata                         2023c  h71feb2d_0          conda-forge/noarch       Cached
  + wheel                         0.40.0  pyhd8ed1ab_0        conda-forge/noarch       Cached
  + xz                             5.2.6  h166bdaf_0          conda-forge/linux-64     Cached
  + zlib                          1.2.13  hd590300_5          conda-forge/linux-64     Cached
  + zstd                           1.5.2  hfc55251_7          conda-forge/linux-64      431kB

  Summary:

  Install: 71 packages

  Total download: 40MB

...

Either way, we can totally loosen the depenency pinnings on the recipe.

[bede]

Bowtie2 doesn't seem to pin a python version? https://github.com/bioconda/bioconda-recipes/blob/master/recipes/bowtie2/meta.yaml

Pin was inaccurate, but the recipe seems to require >=3.10,<3.11.0a0. I've asked about this on Gitter but no answers surfaced.

Interesting that neither of you can replicate this issue. I can also replicate on a fresh 22.04 VM with miniconda, mamba installed and bioconda following usage guidelines. Also just rep'd with fresh micromamba install. Is there something basic I'm missing wrt setup?

I've just tested with older min versions for the pyproject.toml deps so could push these and make a new tag and update the recipe? Will the recipe update automatically if I create releases properly with GitHub @rpetit3 ? That would be handy.

Thanks both 🙏

[bede]

Hold the phone, I see auto updates are already working 🙌 https://github.com/bioconda/bioconda-recipes/pull/41967

[bede]

Ok, my mistake, just needed -c conda-forge in my command. Micromamba working great!

[rpetit3]

No worries @bede, that's an easy fix!