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README.md

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phpMs
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=====
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phpMs is PHP-based free open-source library for proteomics. The library contains a core set of classes for storing common data such as spectra, peptides and proteins. In addition the library contains a number of readers and/or writers for common file formats, including MGF, FASTA, mzIdentML, proBed. The library also contains a number of useful utiltities for performing protein digestion, peptide fragmentation, and search engine intergration.
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phpMs is PHP-based free open-source library for proteomics. The library contains a core set of classes for storing common data such as spectra, peptides and proteins. In addition the library contains a number of readers and/or writers for common file formats, including MGF, FASTA, mzIdentML, proBed. The library also contains a number of useful utilities for performing protein digestion, peptide fragmentation, and search engine integration.
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![Build Status](http://pgb.liv.ac.uk/jenkins/buildStatus/icon?job=php-ms)
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![Quality Gate](http://pgb.liv.ac.uk/ci/phpMs/badge/gate.svg)
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------------
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- PHP Version 5.4+
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- ext/xsl
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Install
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-------
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Composer Installation
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---------------------
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phpMs can be used with [Composer](https://getcomposer.org/) and is available via [Packagist](https://packagist.org/packages/pgb-liv/php-ms).
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To install the library use [Composer](https://getcomposer.org/)
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composer require pgb-liv/php-ms
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Or add it to your existing composer.json:
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"require" : {
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"pgb-liv/php-ms" : "dev-master"
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},
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Git Installation
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----------------
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For non-composer users or phpMs developers, phpMs source can be pulled directly.
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git clone git://github.com/PGB-LIV/php-ms.git
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composer install
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"require" : {
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"pgb-liv/php-ms" : "1.*"
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},
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The composer install will add any dependencies required to run tests.
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Releases made available by GitHub ande the GitHub source do not include depedency code. It is recommended you always use phpMs via Composer.
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API Documentation
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-----------------

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