1 year ago

#72407

test-img

O.rka

How to specify channel-specific package dependencies in conda package meta.yaml?

I've been following the tutorials here:

I can't figure out how to make package dependencies for my conda package.

Here's my meta.yaml:

{% set name = "fastq_preprocessor" %}
{% set version = "2022.01.19" %}

package:
  name: {{ name|lower }}
  version: {{ version }}
  script: python -m pip install --no-deps --ignore-installed .

source:
  url: https://github.com/jolespin/fastq_preprocessor/releases/download/v2022.01.19/fastq_preprocessor-2022.1.19.tar.gz

build:
  noarch: python
  number: 0

requirements:
  build:
    - python >=3.6
    - setuptools
  run:
    - python >=3.6

about:
  home: https://github.com/jolespin/fastq_preprocessor
  license: BSD-3
  license_family: BSD
  license_file: LICENSE.txt
  summary: 'A fastq preprocessor for short read sequencing'
  description: 'A fastq preprocessor for short read sequencing. Can be used as a wrapper around fastp for a standardized directory structure or can feed the trimmed reads into bowtie2 if an index is provided to decontaminate sequences similar to kneaddata (useful in metagenomics to remove host reads). Also includes functionality to filter based on k-mer profiles and is useful for quantifying the amount of ribosomal reads. At each stage, seqkit stats is run so there are read stats that can be used post hoc.'

For example, I want the installation to install: fastp, bbmap, etc. from bioconda package and pandas from conda-forge.

How do I add these channel-specific dependencies into my meta.yaml so it installs them when the package is installed?

I thought about doing a conda env export and then copy and pasting but I don't that's how it works.

python

package

conda

conda-build

0 Answers

Your Answer

Accepted video resources