:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'squire' .. highlight: bash squire ====== .. conda:recipe:: squire :replaces_section_title: :noindex: Quantitative\, locus\-specific view of transposable element expression. :homepage: https://github.com/wyang17/SQuIRE :license: GNU :recipe: /`squire `_/`meta.yaml `_ .. conda:package:: squire |downloads_squire| |docker_squire| :versions: ``0.9.9.92-1``,  ``0.9.9.92-0`` :depends bedtools: ``2.25.0`` :depends bioconductor-biocparallel: ``1.12.0`` :depends bioconductor-deseq2: ``1.16.1`` :depends bioconductor-vsn: :depends igvtools: ``2.3.93`` :depends pyfaidx: :depends python: ``2.7.*`` :depends r-base: ``3.4.1`` :depends r-ggrepel: :depends r-hexbin: :depends r-pheatmap: :depends samtools: ``1.1`` :depends star: ``2.5.3a`` :depends stringtie: ``1.3.3`` :depends ucsc-bedgraphtobigwig: :depends ucsc-genepredtobed: :depends ucsc-genepredtogtf: :depends ucsc-gtftogenepred: :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 squire and update with:: mamba update squire To create a new environment, run:: mamba create --name myenvname squire 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/squire: (see `squire/tags`_ for valid values for ````) .. |downloads_squire| image:: https://img.shields.io/conda/dn/bioconda/squire.svg?style=flat :target: https://anaconda.org/bioconda/squire :alt: (downloads) .. |docker_squire| image:: https://quay.io/repository/biocontainers/squire/status :target: https://quay.io/repository/biocontainers/squire .. _`squire/tags`: https://quay.io/repository/biocontainers/squire?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/squire/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/squire/README.html