Conda installation

[rivera10]

Hello,

Great tool! Would it be possible to have a Bioconda recipe for Ratatosk? This way it will also trigger the creation of Biocontainers (docker and singularity) that can be integrated in assembly pipelines. Thanks

Best, Ramon

[GuillaumeHolley]

Hi @rivera10,

I am not very familiar with bioconda in general (I only did one bioconda recipe so far) but I can surely come up with something :) I'll keep the issue open while it is in progress and will let you know here as soon as it is ready.

Guillaume

[rivera10]

Hello @GuillaumeHolley,

Thanks for the fast answer. For bioconda here is basically what you need.

1- Fork repository 2- Create a directory for ratatosk under the recipes directory (i.e. bioconda-recipes/recipes/ratatosk) 3- Create file meta.yaml (i.e. bioconda-recipes/recipes/ratatosk/meta.yaml) For ratatosk will be like this

{% set name = 'Ratatosk' %}
{% set version = '0.1' %}

package:
  name: {{ name }}
  version: {{ version }}

build:
  number: 0

source:
  url: https://github.com/DecodeGenetics/Ratatosk/archive/{{ version }}.tar.gz
  sha256: 9b82c6875e3613b12ecdc264eaa7c920da5c7ba7256e95ab5528dbdb65e4cc90

requirements:
  build:
    - {{ compiler('c') }}
    - {{ compiler('cxx') }}
    - cmake
  host:
    - zlib
  run:
    - zlib

test:
  commands:
    - Ratatosk --help

about:
  home: https://github.com/DecodeGenetics/Ratatosk
  license: BSD-2-Clause
  license_file: LICENSE
  summary: "Ratatosk is a phased error correction tool for erroneous long reads based on compacted and colored de Bruijn graphs built from accurate short reads."

4- Create file build.sh (i.e. bioconda-recipes/recipes/ratatosk/build.sh)

5- Create a PR to the bioconda:master and follow the instructions they give in the PR page.

Hope this can help.

Ramon

[rivera10]

I forgot to add the content of the build.sh. It should look similar to this

mkdir -p $PREFIX/bin
mkdir build && cd build
cmake -DCMAKE_INSTALL_PREFIX=$PREFIX/bin ..
make
make install

If you have issues with the zlib see here

[loraine-gueguen]

Hi, I have started a Bioconda recipe for Ratatosk: https://github.com/bioconda/bioconda-recipes/pull/37864 (Thanks for the snippets above, and feel free to participate!) However, it fails on build with: CMake Error: The source directory "/opt/conda/conda-bld/ratatosk_1667903456105/work/Bifrost/build/DENABLE_AVX2=OFF" does not exist. Shouldn't the DENABLE_AVX2=OFF option be preceded with - in the following line ? https://github.com/DecodeGenetics/Ratatosk/blob/b08613bc947a3df628b2c2f018414e0e6d6f8593/src/CMakeLists.txt#L15

Regards