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Readme / Documentation for `NucleoMiner2` |
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***************************************** |
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`NucleoMiner2` offers Python API and R package allowing to perform |
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quantitative analysis of nucleosomal epigenome. It is especially well |
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suited for scripting to extract natural Single-Nucleosome Epi- |
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Polymorphisms (SNEP) from ChIP-Seq data. |
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`NucleoMiner2` offers Python API and R package allowing to perform quantitative analysis of epigenetic marks on individual nucleosomes. It was developed to detect natural Single-Nucleosome Epi-Polymorphisms (SNEP) from MNase-seq and ChIP-seq data. |
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License |
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======= |
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Copyright CNRS 2012-2013
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- Florent CHUFFART
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- Jean-Baptiste VEYRIERAS
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- Gael YVERT
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Copyright CNRS 2012-2013 |
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- Florent CHUFFART |
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- Jean-Baptiste VEYRIERAS |
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- Gael YVERT |
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This software is a computer program which purpose is to perform quanti- |
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tative analysis of epigenetic marks at single nucleosome resolution. |
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This software is governed by the CeCILL license under French law and |
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abiding by the rules of distribution of free software. You can use, |
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modify and/ or redistribute the software under the terms of the CeCILL |
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license as circulated by CEA, CNRS and INRIA at the following URL |
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"http://www.cecill.info". |
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As a counterpart to the access to the source code and rights to copy, |
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modify and redistribute granted by the license, users are provided only |
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with a limited warranty and the software's author, the holder of the |
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economic rights, and the successive licensors have only limited |
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liability. |
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In this respect, the user's attention is drawn to the risks associated |
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with loading, using, modifying and/or developing or reproducing the |
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software by the user in light of its specific status of free software, |
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that may mean that it is complicated to manipulate, and that also |
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therefore means that it is reserved for developers and experienced |
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professionals having in-depth computer knowledge. Users are therefore |
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encouraged to load and test the software's suitability as regards their |
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requirements in conditions enabling the security of their systems and/or |
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data to be ensured and, more generally, to use and operate it in the |
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same conditions as regards security. |
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The fact that you are presently reading this means that you have had |
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knowledge of the CeCILL license and that you accept its terms. |
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tative analysis of epigenetic marks at single nucleosome resolution. |
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This software is governed by the CeCILL license under French law and |
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abiding by the rules of distribution of free software. You can use, |
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modify and/ or redistribute the software under the terms of the CeCILL |
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license as circulated by CEA, CNRS and INRIA at the following URL |
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"http://www.cecill.info". |
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As a counterpart to the access to the source code and rights to copy, |
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modify and redistribute granted by the license, users are provided only |
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with a limited warranty and the software's author, the holder of the |
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economic rights, and the successive licensors have only limited |
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liability. |
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This software is provided with absolutely NO WARRANTY. The authors can not be held responsible, even partially, for any damage, loss, financial loss or any other undesired facts resulting from the use of the software. |
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In this respect, the user's attention is drawn to the risks associated |
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with loading, using, modifying and/or developing or reproducing the |
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software by the user in light of its specific status of free software, |
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that may mean that it is complicated to manipulate, and that also |
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therefore means that it is reserved for developers and experienced |
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professionals having in-depth computer knowledge. Users are therefore |
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encouraged to load and test the software's suitability as regards their |
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requirements in conditions enabling the security of their systems and/or |
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data to be ensured and, more generally, to use and operate it in the |
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same conditions as regards security. |
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The fact that you are presently reading this means that you have had |
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knowledge of the CeCILL license and that you accept its terms. |
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Installation Instructions |
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========================= |
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Links |
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----- |
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`NucleoMiner2` home page and documentation: https://forge.cbp.ens-lyon.fr/redmine/projects/nucleominer |
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`NucleoMiner2` home page and documentation are available here: |
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- https://forge.cbp.ens-lyon.fr/redmine/projects/nucleominer |
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The Yvert lab web page is accessible here: |
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Gael Yvert lab page: http://www.ens-lyon.fr/LBMC/gisv/
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- http://www.ens-lyon.fr/LBMC/gisv/
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Installation |
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------------ |
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- Download archive |
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- Compile bowtie2 |
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- Compile samtools |
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- Compile bedtools |
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- Compile TemplateFilter |
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The first installation step is to retrieve the source code of MyLabStocks. You can do this by typing the following command in a terminal. |
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.. code:: bash |
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git clone http://forge.cbp.ens-lyon.fr/git/nucleominer |
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.. |
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Prerequisites |
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^^^^^^^^^^^^^ |
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To work properly, NucleoMiner2 needs that the following free software are installed and made available on your system: |
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- Bowtie2 http://bowtie-bio.sourceforge.net/bowtie2 |
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- SAMtools http://samtools.sourceforge.net |
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- bedtools http://code.google.com/p/bedtools/ |
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- TemplateFilter http://compbio.cs.huji.ac.il/NucPosition/TemplateFiltering |
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It also requires the following R packages to be installed on your system: |
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Required R packages: |
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- bot |
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- fork |
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- rjson |
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- seqinr |
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- cachecache |
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- cachecache https://forge.cbp.ens-lyon.fr/redmine/projects/cachecache |
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- bot https://forge.cbp.ens-lyon.fr/redmine/projects/bot |
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- nucleominer https://forge.cbp.ens-lyon.fr/redmine/projects/nucleominer |
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The first packages could be installed by typing the following command in an R console: |
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The last packages are available in the git repository they could be install by typing the following command in your terminal: |
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.. code:: bash |
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cd src/r_packages/ |
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tar xfvz R-latest.tar.gz |
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cd R-patched |
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./configure --with-x=no PDFLATEX="ls" |
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make |
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cd ../../.. |
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R_BIN=src/r_packages/R-patched/bin/R |
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$R_BIN CMD INSTALL src/r_packages/rjson_0.2.12.tar.gz |
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$R_BIN CMD INSTALL src/r_packages/seqinr_3.0-7.tar.gz |
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$R_BIN CMD INSTALL src/r_packages/plotrix_3.4-5.tar.gz |
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$R_BIN CMD INSTALL src/r_packages/nm_2.0.tar.gz |
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$R_BIN CMD INSTALL src/r_packages/fork_1.2.4.tar.gz |
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$R_BIN CMD INSTALL src/r_packages/bot_0.9.tar.gz |
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$R_BIN CMD INSTALL src/r_packages/DESeq_1.14.0.tar.gz |
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... |
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usage |
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===== |
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See html documentation for `NucleoMiner2`: http://www.ens-lyon.fr/LBMC/gisv/ |
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cd nucleominer |
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R CMD INSTALL doc/Chuffart_NM2_workdir/deps/bot_0.14.tar.gz\ |
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doc/Chuffart_NM2_workdir/deps/cachecache_0.1.tar.gz\ |
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build/nucleominer_2.XXX.tar.gz |
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