/q2-assembly

QIIME 2 plugin for (meta)genome assembly.

Primary LanguagePythonBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

q2-assembly

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QIIME 2 plugin for (meta)genome assembly.

Installation

Before q2-assembly is available from conda, follow the installation steps described below.

curl -sLH 'Accept: application/vnd.github.v3.raw' https://api.github.com/repos/bokulich-lab/q2-assembly/contents/requirements.txt > requirements.txt
mamba create -yn q2-shotgun \
  -c https://packages.qiime2.org/qiime2/2022.4/tested \
  -c bioconda -c conda-forge -c default \
  --file requirements.txt

conda activate q2-shotgun

Additionally, a patched version of quast is required, plus q2-types-genomics and q2-assembly itself:

pip install \
  git+https://github.com/ablab/quast.git@de7e1f4891a3487f3c0df6ae27cbfba38734d686 \
  git+https://github.com/bokulich-lab/q2-assembly.git

Refresh cache and check that everything worked:

qiime dev refresh-cache
qiime info