:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'tpp' .. highlight: bash tpp === .. conda:recipe:: tpp :replaces_section_title: :noindex: The Trans\-Proteomic Pipeline \(TPP\) is a collection of integrated tools for MS\/MS proteomics developed at the Seattle Proteome Center. The Bioconda package includes the command\-line versions of the TPP toolset. These programs include tools for validation \(PeptideProphet\, iProphet\, ProteinProphet\, Mayu\) and quantification \(XPRESS\, ASAPRatio\, Libra\) as well as a number of parsers and converters \(Out2XML\, Mascot2XML\, Tandem2XML\, etc\). :homepage: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP :license: GPL v. 2.0 and LGPL :recipe: /`tpp `_/`meta.yaml `_ .. conda:package:: tpp |downloads_tpp| |docker_tpp| :versions: ``5.0.0-0`` :depends bzip2: ``1.0*`` :depends hardklor: :depends libgcc: ``<=4.9`` :depends perl: ``5.22.0*`` :depends perl-findbin-libs: :depends perl-xml-parser: :depends zlib: ``1.2.11*`` :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 tpp and update with:: mamba update tpp To create a new environment, run:: mamba create --name myenvname tpp 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/tpp: (see `tpp/tags`_ for valid values for ````) .. |downloads_tpp| image:: https://img.shields.io/conda/dn/bioconda/tpp.svg?style=flat :target: https://anaconda.org/bioconda/tpp :alt: (downloads) .. |docker_tpp| image:: https://quay.io/repository/biocontainers/tpp/status :target: https://quay.io/repository/biocontainers/tpp .. _`tpp/tags`: https://quay.io/repository/biocontainers/tpp?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/tpp/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/tpp/README.html