:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'targqc' .. highlight: bash targqc ====== .. conda:recipe:: targqc :replaces_section_title: :noindex: Target capture coverage QC :homepage: https://github.com/vladsaveliev/TargQC :license: GPL3 / GNU General Public License v3 (GPLv3) :recipe: /`targqc `_/`meta.yaml `_ .. conda:package:: targqc |downloads_targqc| |docker_targqc| :versions: ``1.8.1-1``,  ``1.8.1-0``,  ``1.4.4-1``,  ``1.4.4-0`` :depends beautifulsoup4: :depends bedtools: ``>=2.25`` :depends bwa: :depends click: :depends coverage: :depends gffutils: :depends ipyparallel: :depends ipython: :depends ipython-cluster-helper: :depends joblib: :depends lxml: :depends natsort: :depends nose: :depends numpy: :depends pandas: :depends pip: :depends pybedtools: :depends pysam: :depends python: ``>=3.6`` :depends qualimap: :depends sambamba: ``>=0.7.0`` :depends six: :depends tempita: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`set-up-channels`). While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see `here `_ for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others. Given that you already have a conda environment in which you want to have this package, install with:: mamba install targqc and update with:: mamba update targqc To create a new environment, run:: mamba create --name myenvname targqc with ``myenvname`` being a reasonable name for the environment (see e.g. the `mamba docs `_ for details and further options). Alternatively, use the docker container:: docker pull quay.io/biocontainers/targqc: (see `targqc/tags`_ for valid values for ````) .. |downloads_targqc| image:: https://img.shields.io/conda/dn/bioconda/targqc.svg?style=flat :target: https://anaconda.org/bioconda/targqc :alt: (downloads) .. |docker_targqc| image:: https://quay.io/repository/biocontainers/targqc/status :target: https://quay.io/repository/biocontainers/targqc .. _`targqc/tags`: https://quay.io/repository/biocontainers/targqc?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/targqc/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/targqc/README.html