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---
layout: frozen
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index: imp$Integrated Metaomic Pipeline
nav: ../index$Frozen pages
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theme: paper
type: frozen
title: Frozen IMP
description: <b>I</b>ntegrated <b>M</b>etaomic <b>P</b>ipeline
---

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                <rtitle>A computational framework for integrative metagenomic and metatranscriptomic analyses</rtitle>
                <hr></hr>
                <rdoi>DOI: [ <a href="">doi:10.10.1038/nphys1170</a>) ]</rdoi>
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                <h4><span class="glyphicon glyphicon-globe" aria-hidden="true"></span><rtitle>Website</rtitle></h4>
                <hr></hr>
                <rbody>The <b>IMP</b> website hosted within <b>R3lab</b> frame is available <a href="http://r3lab.uni.lu/web/imp/index.html">
                    here</a>.
                </rbody>
            </div>
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                <h4><span class="glyphicon glyphicon-duplicate" aria-hidden="true"></span><rtitle>Source code</rtitle></h4>
                <hr></hr>
                <rbody>The source code is available on the <a href="https://git-r3lab.uni.lu/shaman.narayanasamy/IMP">LCSB Gitlab</a> where you can traceback what have been done by the authors.</rbody>
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                <h4><span class="glyphicon glyphicon-cog" aria-hidden="true"></span><rtitle>Workflow</rtitle></h4>
                <hr></hr>
                <rbody>Snakemake, a reproducible workflow engine that allow us IMP users execute the same workflow for each analysis.
                    From <a href="http://bioinformatics.oxfordjournals.org/content/28/19/2520">Köster, Johannes and Rahmann,
                    Sven. “Snakemake - A scalable bioinformatics workflow engine”. Bioinformatics 2012.</a>
                </rbody>
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                <h4><span class="glyphicon glyphicon-level-up" aria-hidden="true"></span><rtitle>Data repository</rtitle></h4>
                <hr></hr>
                <rbody>The <b>IMP</b> data repository is hosted on the <a href="https://webdav-r3lab.uni.lu/public/R3lab/IMP/">
                    LCSB webdav storage</a>. You will find some of the tools installed within IMP.
                    IMP versions are stored under the <b>dist</b> folder.
                </rbody>
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                <h4><span class="glyphicon glyphicon-th" aria-hidden="true"></span><rtitle>Environment</rtitle></h4>
                <hr></hr>
                <rbody>All tools dependencies of IMP are frozen inside a docker container.
                    The files used to build the container can be found on Gitlab and versioned tarballs of the
                    containers are found under the <a href="https://webdav-r3lab.uni.lu/public/R3lab/IMP/dist/">webdav</a>.
                </rbody>
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                <h4><span class="glyphicon glyphicon-repeat" aria-hidden="true"></span><rtitle>R toolkit</rtitle></h4>
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                <rbody>
                    We use the <a href="https://cran.r-project.org/web/packages/checkpoint/vignettes/checkpoint.html">
                    checkpoint</a> library to ensure that all of the necessary R packages are installed
                    with the correct versions.
                </rbody>
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                <h4><span class="glyphicon glyphicon-book" aria-hidden="true"></span><rtitle>Report</rtitle></h4>
                <hr></hr>
                <rbody>
                    <b>IMP</b> report contains all information needed to reproduce the same workflow, from the version
                    of <b>IMP</b> used to make the analysis to the configuration file used to start the workflow.
                    Everything is condensed and organized within an HTML report. Some reports can be found
                    <a href="https://webdav-r3lab.uni.lu/public/R3lab/IMP/reports/">here</a>.
                </rbody>
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