conda recepies #62

BarryDigby · 2022-10-28T19:11:29Z

nf-core/circrna modules that require package builds for the conda repository:

CIRIquant

Not working because argparse>=1.2.1 and scipy==1.2.2 are not found using defaults/conda-forge/bioconda.

argparse>=1.2.1 is available from this channel: pdrops::argparse==1.2.2 but I cannot figure out how to tell my build to incorporate this channel. I have added it to my local conda config, to no avail...

scipy==1.2.2 does not exist on conda.

I have tried both pypi skeletons and generic noarch python skeletons here, so I am not sure how to proceed.

circtools

PR: bioconda/bioconda-recipes#37786

posterity..

PR: bioconda/bioconda-recipes#37786

The author of DCC made a pypi package called circtools available at https://pypi.org/project/circtools/. This is convenient for me as it bundles DCC and CircTest together, both of which are used in the workflow.

grayskull pypi circtools
conda build recipes/circtools

Successfully builds, pushed to anaconda to test

conda config --set anaconda_upload yes
anaconda upload \
    /Users/bdigby/opt/anaconda3/conda-bld/osx-64/circtools-1.2.1-py39_0.tar.bz2

TODO: This package works as expected, but I need it to be hosted by bioconda and not b.digby
https://anaconda.org/b.digby/circtools

bioconda-utils build --docker --mulled-test --packages recipes/circtools fails, see below:

error log

(bioconda) bdigby@sr-loaner-c02ytamllvcf bioconda-recipes % bioconda-utils build --docker --mulled-test --packages circtools
14:40:40 BIOCONDA INFO Considering total of 1 recipes (circtools).
14:40:40 BIOCONDA INFO Processing 1 recipes (circtools).
14:40:41 BIOCONDA INFO Generating DAG
Loading Recipes: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 69.64it/s]
14:40:41 BIOCONDA INFO 1 recipes to build and test: 
circtools
14:40:41 BIOCONDA INFO Determining expected packages for recipes/circtools
Setting build platform. This is only useful when pretending to be on another platform, such as for rendering necessary dependencies on a non-native platform. I trust that you know what you're doing.
14:40:41 CONDA_BUILD WARNING Setting build platform. This is only useful when pretending to be on another platform, such as for rendering necessary dependencies on a non-native platform. I trust that you know what you're doing.
Updating build index: /Users/bdigby/opt/anaconda3/envs/bioconda/conda-bld

No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.16
14:40:41 CONDA_BUILD WARNING No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.16
Adding in variants from internal_defaults
14:40:41 CONDA_BUILD INFO Adding in variants from internal_defaults
Adding in variants from /Users/bdigby/opt/anaconda3/envs/bioconda/conda_build_config.yaml
14:40:41 CONDA_BUILD INFO Adding in variants from /Users/bdigby/opt/anaconda3/envs/bioconda/conda_build_config.yaml
Adding in variants from /Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml
14:40:41 CONDA_BUILD INFO Adding in variants from /Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml
defaults/noarch: 4.77MB [00:00, 30.2MB/s]                                                                                      | 0/9 [00:00<?, ?files/s]
defaults/linux: 33.5MB [00:00, 39.3MB/s]                                                                               | 1/9 [00:00<00:03,  2.61files/s]
bioconda/linux: 29.0MB [00:01, 16.4MB/s]▍                                                                              | 2/9 [00:01<00:07,  1.07s/files]
defaults/osx: 30.8MB [00:03, 10.0MB/s]█████████████▋                                                                   | 3/9 [00:03<00:06,  1.07s/files]
conda-forge/noarch: 69.2MB [00:04, 16.6MB/s]██████████████████▉                                                        | 4/9 [00:04<00:06,  1.20s/files]
bioconda/osx: 23.4MB [00:04, 5.89MB/s]MB/s]]
bioconda/noarch: 26.1MB [00:00, 86.9MB/s]█████████████████████████████████                                             | 5/9 [00:08<00:08,  2.09s/files]
conda-forge/linux: 215MB [00:10, 20.8MB/s]██████████████████████████████████████████████████████▌                      | 7/9 [00:09<00:02,  1.30s/files]
conda-forge/osx: 187MB [00:20, 9.59MB/s]███████████████████████████████████████████████████████████████████▊           | 8/9 [00:19<00:03,  3.83s/files]
Downloading: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████| 9/9 [00:27<00:00,  3.09s/files]
Updating build index: /Users/bdigby/opt/anaconda3/envs/bioconda/conda-bld

Adding in variants from argument_variants
14:41:20 CONDA_BUILD INFO Adding in variants from argument_variants
Attempting to finalize metadata for circtools
14:41:20 CONDA_BUILD INFO Attempting to finalize metadata for circtools
bioconda/noarch                                      3.8MB @   4.0MB/s  1.1s
conda-forge/noarch                                  10.1MB @   4.4MB/s  2.6s
bioconda/osx-64                                      3.7MB @   1.3MB/s  2.9s
conda-forge/osx-64                                  24.7MB @   4.9MB/s  6.1s
Reloading output folder: /Users/bdigby/opt/anaconda3/envs/bioconda/conda-bld
Users/bdigby/opt/anaconda3/envs/bioconda/conda-b..  ??.?MB @  ??.?MB/s 0 failed  0.0s
Users/bdigby/opt/anaconda3/envs/bioconda/conda-b.. 127.0 B @ 296.0kB/s  0.0s
Transaction

  Prefix: /Users/bdigby/opt/anaconda3/envs/bioconda

  Nothing to do

Reloading output folder: /Users/bdigby/opt/anaconda3/envs/bioconda/conda-bld
Users/bdigby/opt/anaconda3/envs/bioconda/conda-b..  ??.?MB @  ??.?MB/s 0 failed  0.0s
Users/bdigby/opt/anaconda3/envs/bioconda/conda-b.. 127.0 B @   1.2MB/s  0.0s
Transaction

  Prefix: /Users/bdigby/opt/anaconda3/envs/bioconda

  Updating specs:

   - pip
   - python=3.9[build=*_cpython]


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

  + bzip2                1.0.8  h0d85af4_4          conda.anaconda.org.-a24869bc-cf14-4239-84c7-1b52b5a11e95/conda-forge/osx-64     159kB
  + ca-certificates  2022.9.24  h033912b_0          conda.anaconda.org.-a24869bc-cf14-4239-84c7-1b52b5a11e95/conda-forge/osx-64     154kB
  + libffi               3.4.2  h0d85af4_5          conda.anaconda.org.-a24869bc-cf14-4239-84c7-1b52b5a11e95/conda-forge/osx-64      51kB
  + libsqlite           3.39.4  ha978bb4_0          conda.anaconda.org.-a24869bc-cf14-4239-84c7-1b52b5a11e95/conda-forge/osx-64     891kB
  + libzlib             1.2.13  hfd90126_4          conda.anaconda.org.-a24869bc-cf14-4239-84c7-1b52b5a11e95/conda-forge/osx-64      66kB
  + ncurses                6.3  h96cf925_1          conda.anaconda.org.-a24869bc-cf14-4239-84c7-1b52b5a11e95/conda-forge/osx-64     937kB
  + openssl              3.0.7  hfd90126_0          conda.anaconda.org.-a24869bc-cf14-4239-84c7-1b52b5a11e95/conda-forge/osx-64       3MB
  + pip                   22.3  pyhd8ed1ab_0        conda.anaconda.org.-a24869bc-cf14-4239-84c7-1b52b5a11e95/conda-forge/noarch       2MB
  + python              3.9.13  hf8d34f4_0_cpython  conda.anaconda.org.-a24869bc-cf14-4239-84c7-1b52b5a11e95/conda-forge/osx-64      13MB
  + readline             8.1.2  h3899abd_0          conda.anaconda.org.-a24869bc-cf14-4239-84c7-1b52b5a11e95/conda-forge/osx-64     272kB
  + setuptools          65.5.0  pyhd8ed1ab_0        conda.anaconda.org.-a24869bc-cf14-4239-84c7-1b52b5a11e95/conda-forge/noarch     787kB
  + sqlite              3.39.4  h9ae0607_0          conda.anaconda.org.-a24869bc-cf14-4239-84c7-1b52b5a11e95/conda-forge/osx-64     897kB
  + tk                  8.6.12  h5dbffcc_0          conda.anaconda.org.-a24869bc-cf14-4239-84c7-1b52b5a11e95/conda-forge/osx-64       4MB
  + tzdata               2022f  h191b570_0          conda.anaconda.org.-a24869bc-cf14-4239-84c7-1b52b5a11e95/conda-forge/noarch     121kB
  + wheel               0.37.1  pyhd8ed1ab_0        conda.anaconda.org.-a24869bc-cf14-4239-84c7-1b52b5a11e95/conda-forge/noarch      32kB
  + xz                   5.2.6  h775f41a_0          conda.anaconda.org.-a24869bc-cf14-4239-84c7-1b52b5a11e95/conda-forge/osx-64     238kB

  Summary:

  Install: 16 packages

  Total download: 26MB

───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

Traceback (most recent call last):
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/bin/bioconda-utils", line 10, in <module>
    sys.exit(main())
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/bioconda_utils/cli.py", line 971, in main
    bioconductor_skeleton, clean_cran_skeleton, autobump, bot
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/argh/dispatching.py", line 328, in dispatch_commands
    dispatch(parser, *args, **kwargs)
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/argh/dispatching.py", line 174, in dispatch
    for line in lines:
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/argh/dispatching.py", line 277, in _execute_command
    for line in result:
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/argh/dispatching.py", line 260, in _call
    result = function(*positional, **keywords)
  File "<boltons.funcutils.FunctionBuilder-5>", line 2, in build
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/bioconda_utils/cli.py", line 130, in wrapper
    func(*args, **kwargs)
  File "<boltons.funcutils.FunctionBuilder-4>", line 2, in build
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/bioconda_utils/cli.py", line 59, in wrapper
    func(*args, **kwargs)
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/bioconda_utils/cli.py", line 476, in build
    keep_old_work=keep_old_work)
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/bioconda_utils/build.py", line 320, in build_recipes
    pkg_paths = utils.get_package_paths(recipe, check_channels, force=force)
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/bioconda_utils/utils.py", line 1126, in get_package_paths
    platform, metas = _load_platform_metas(recipe, finalize=True)
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/bioconda_utils/utils.py", line 1035, in _load_platform_metas
    return platform, load_all_meta(recipe, config=config, finalize=finalize)
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/bioconda_utils/utils.py", line 447, in load_all_meta
    for non_finalized_meta in metas
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/bioconda_utils/utils.py", line 453, in <listcomp>
    bypass_env_check=False,
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/conda_build/api.py", line 52, in render
    bypass_env_check=bypass_env_check):
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/conda_build/metadata.py", line 2122, in get_output_metadata_set
    bypass_env_check=bypass_env_check)
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/conda_build/metadata.py", line 782, in finalize_outputs_pass
    permit_unsatisfiable_variants=permit_unsatisfiable_variants)
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/conda_build/render.py", line 548, in finalize_metadata
    exclude_pattern)
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/conda_build/render.py", line 409, in add_upstream_pins
    permit_unsatisfiable_variants, exclude_pattern)
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/conda_build/render.py", line 375, in _read_upstream_pin_files
    permit_unsatisfiable_variants=permit_unsatisfiable_variants)
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/conda_build/render.py", line 148, in get_env_dependencies
    channel_urls=tuple(m.config.channel_urls))
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/boa/cli/mambabuild.py", line 124, in mamba_get_install_actions
    solution = solver.solve_for_action(_specs, prefix)
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/boa/core/solver.py", line 242, in solve_for_action
    self.index + self.local_index,
  File "/Users/bdigby/opt/anaconda3/envs/bioconda/lib/python3.7/site-packages/boa/core/solver.py", line 79, in to_action
    entry = lookup_dict[get_url_from_channel(c)]
KeyError: 'https://conda.anaconda.org.-a24869bc-cf14-4239-84c7-1b52b5a11e95/conda-forge/osx-64'

find_circ

PR: bioconda/bioconda-recipes#37923

circrna_finder

PR: bioconda/bioconda-recipes#37922

targetscan

PR: bioconda/bioconda-recipes#37960

I cannot find a license file for targetscan, and it is denoted as being Copyright (c) The Whitehead Institute of Biomedical Research.

Is it appropriate to add this to bioconda? If not, how can I proceed to ensure I am following nf-core best practices?

DEA

Mulled container for differential exp scripts. PR: BioContainers/multi-package-containers#2382

The text was updated successfully, but these errors were encountered:

BarryDigby · 2022-11-14T18:47:07Z

Hi @apeltzer, I was away at a conference last week but have got around to creating PRs to add tools to bioconda. Have you permission to review and merge the above PRs?

Two areas of concern are detailed above, any guidance here would be greatly appreciated

apeltzer · 2022-11-16T14:12:36Z

I have

apeltzer · 2022-11-23T12:50:38Z

Hi @BarryDigby - just checked (sorry, super busy time right now at work): It looks quite good at the moment to me, e.g. targetscan biocontainer is here: https://quay.io/repository/biocontainers/targetscan

apeltzer · 2022-11-23T12:57:38Z

After x-checking, it seems not to have been uploaded - we should maybe ask in their Support Channel. I also opened an issue on bioconda to ask if something was odd there.

See here: bioconda/bioconda-recipes#38099

BarryDigby · 2022-11-23T19:30:14Z

@apeltzer Really appreciate you taking the time to check Alex. The conversion to DSL2 is going pretty smoothly, it's just the containers that are holding up the show (and linting, probably 🤖 ). Trying my best to have it ready for review next week

BarryDigby · 2022-11-29T11:08:35Z

@apeltzer Hey Alex, the workflow has been successfully converted to DSL2, the only catch being I am still waiting on those bioconda containers, and for a reason I cannot pin down, singularity fails to pull this image from quay despite it working perfectly fine for Docker. Irritating to say the least 😁

Given the deadline for the response to authors for BMC is December 5th... what's the gameplan here?

apeltzer · 2022-11-30T10:22:57Z

Just asked on the bioconda chat to unhide these & also asked whats going on with Singularity.

apeltzer · 2022-11-30T12:55:15Z

Singularity there in << 24hours, the quay.io should already be there. So "just" in time :-D

BarryDigby added bug Something isn't working enhancement Improvement for existing functionality and removed bug Something isn't working labels Oct 28, 2022

apeltzer mentioned this issue Nov 23, 2022

Missing containers for recipes? bioconda/bioconda-recipes#38099

Closed

apeltzer closed this as completed Dec 13, 2022

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

conda recepies #62

conda recepies #62

BarryDigby commented Oct 28, 2022 •

edited

Loading

BarryDigby commented Nov 14, 2022

apeltzer commented Nov 16, 2022

apeltzer commented Nov 23, 2022

apeltzer commented Nov 23, 2022

BarryDigby commented Nov 23, 2022

BarryDigby commented Nov 29, 2022

apeltzer commented Nov 30, 2022

apeltzer commented Nov 30, 2022

conda recepies #62

conda recepies #62

Comments

BarryDigby commented Oct 28, 2022 • edited Loading

BarryDigby commented Nov 14, 2022

apeltzer commented Nov 16, 2022

apeltzer commented Nov 23, 2022

apeltzer commented Nov 23, 2022

BarryDigby commented Nov 23, 2022

BarryDigby commented Nov 29, 2022

apeltzer commented Nov 30, 2022

apeltzer commented Nov 30, 2022

BarryDigby commented Oct 28, 2022 •

edited

Loading