Révision f78441a4 README
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***************************************** |
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Readme / Documentation for `MyLabsStocks` |
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***************************************** |
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`MyLabsStocks` 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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Readme / Documentation for *MyLabStocks* |
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**************************************** |
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*MyLabStocks* is a web application allowing to easily store, share and |
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retrieve information about molecular biology materials stored in a |
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laboratory. |
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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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- 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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The Software is provided “as is” without warranty of any kind, either |
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express or implied, including without lim- itation any implied warranties |
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of condition, uninterrupted use, merchantability, fitness for a particular |
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purpose, or non-infringement. You use this software at your own risk. |
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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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Copyright CNRS 2012-2013 |
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* Florent CHUFFART |
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* Gael YVERT |
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|
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This software is a computer program which purpose is to perform |
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quantitative analysis of epigenetic marks at single nucleosome |
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resolution. |
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|
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The Software is provided “as is” without warranty of any kind, either |
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express or implied, including without limitation any implied |
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warranties of condition, uninterrupted use, merchantability, fitness |
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for a particular purpose, or non-infringement. You use this software |
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at your own risk. |
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|
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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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| 32 |
license as circulated by CEA, CNRS and INRIA at the following URL |
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"http://www.cecill.info". |
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|
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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 |
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only with a limited warranty and the software's author, the holder |
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of the economic rights, and the successive licensors have only |
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limited liability. |
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|
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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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| 45 |
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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| 47 |
encouraged to load and test the software's suitability as regards |
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| 48 |
their requirements in conditions enabling the security of their |
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systems and/or data to be ensured and, more generally, to use and |
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operate it in the same conditions as regards security. |
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|
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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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This installation has been fully tested on: |
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* Debian 7.2.0 amd64 netinst [1], running on virtual machine using |
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Oracle VM VirtualBox [2] for macosx (dev) |
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* Ubuntu Server 12.04.3 LTSUbuntu server LTS [3], running on |
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physical machine (prod) |
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[1] http://cdimage.debian.org/debian-cd/7.2.0/amd64/iso- |
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cd/debian-7.2.0-amd64-netinst.iso |
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[2] https://www.virtualbox.org |
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[3] http://www.ubuntu.com/download/server |
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Prerequisites |
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------------- |
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sudo apt-get install git mysql-server apache2 php5 phpmyadmin php5-curl csh blast2 tomcat ant openjdk-6-jdk |
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Get MyLabStocks Sources |
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----------------------- |
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git clone http://forge.cbp.ens-lyon.fr/git/mylabstocks |
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`MyLabsStocks` home page: http://www.ens-lyon.fr/LBMC/gisv/ |
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`MyLabsStocks` documentation: http://www.ens-lyon.fr/LBMC/gisv/ |
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Install wwwBlast |
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---------------- |
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MyLabStocks is distributed with wwwblast working on a x64 |
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architecture. For other architectures refer to the NCBI repositories h |
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ttp://mirrors.vbi.vt.edu/mirrors/ftp.ncbi.nih.gov/blast/executables/re |
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lease/LATEST |
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cd mylabstocks/opts/ |
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tar xfvz wwwblast-2.2.26-x64-linux.tar.gz |
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sudo cp -r blast /var/www/. |
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sudo chown www-data:www-data /var/www/blast/TmpGifs /var/www/blast/*.log /var/www/blast/db/ |
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echo "<Directory /var/www/blast/>" > /tmp/blast.conf |
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echo " Options +ExecCGI" >> /tmp/blast.conf |
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echo "</Directory>" >> /tmp/blast.conf |
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echo "AddHandler cgi-script .cgi" >> /tmp/blast.conf |
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sudo cp /tmp/blast.conf /etc/apache2/conf.d/blast.conf |
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rm /tmp/blast.conf |
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sudo /etc/init.d/apache2 restart |
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sudo sed -i 's/<option VALUE.*test_na_db/<option VALUE=oligostock_db>oligostock_db<option VALUE=plasmidstock_db>plasmidstock_db<option VALUE=plfeatstock_db>plfeatstock_db/g' /var/www/blast/blast.html |
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sudo sed -i 's/<option VALUE.*test_aa_db//g' /var/www/blast/blast.html |
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cat /var/www/blast/blast.rc > /tmp/blast.rc |
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echo "blastn oligostock_db" >> /tmp/blast.rc |
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echo "tblastn oligostock_db" >> /tmp/blast.rc |
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echo "tblastx oligostock_db" >> /tmp/blast.rc |
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echo "blastn plasmidstock_db" >> /tmp/blast.rc |
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echo "tblastn plasmidstock_db" >> /tmp/blast.rc |
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echo "tblastx plasmidstock_db" >> /tmp/blast.rc |
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echo "blastn plfeatstock_db" >> /tmp/blast.rc |
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echo "tblastn plfeatstock_db" >> /tmp/blast.rc |
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echo "tblastx plfeatstock_db" >> /tmp/blast.rc |
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sudo cp /tmp/blast.rc /var/www/blast/blast.rc |
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rm /tmp/blast.rc |
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cd ../.. |
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Installation |
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------------ |
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rsync -cauvz --exclude="formatdb.log" --exclude=".DS_Store" ../src/ root@cremone:/var/www/labstocks/ |
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Install PlasMapper |
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------------------ |
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cd /var/www/labstocks |
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# sudo vi connect_entry.php |
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sudo touch formatdb.log |
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sudo chmod 440 connect_entry.php |
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sudo chown -R www-data:www-data connect_entry.php formatdb.log plasmid_files raw_dirs |
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cd mylabstocks/opts/ |
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tar xfvz PlasMapper_download.tar.gz |
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cd PlasMapper |
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# modify installdir as /var/lib/tomcat6 |
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sed -i 's/\/home\/tomcat/\/var\/lib\/tomcat6/g' build.xml |
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# modify servletjar as /usr/share/tomcat6/lib/servlet-api.jar |
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sed -i 's/${installdir}\/common\/lib\/servlet-api.jar/\/usr\/share\/tomcat6\/lib\/servlet-api.jar/g' build.xml
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# change /home/tomcat for /var/lib/tomcat6 |
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sed -i 's/\/home\/tomcat/\/var\/lib\/tomcat6/g' src/ca/ualberta/xdong/plasMapper/annotate/plasMapConfiguration_en_CA.properties |
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# and set blastallDir=/usr/bin/ |
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sed -i 's/\/usr\/local\/bin\//\/usr\/bin\//g' src/ca/ualberta/xdong/plasMapper/annotate/plasMapConfiguration_en_CA.properties |
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# Here PlasMapper is ready to be configured |
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ant clean |
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ant build |
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sudo ant install |
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sudo rm -Rf /var/lib/tomcat6/webapps/PlasMapper/tmp |
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sudo ln -s /tmp/tomcat6-tomcat6-tmp/ /var/lib/tomcat6/webapps/PlasMapper/tmp |
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echo '<?xml version="1.0" encoding="UTF-8"?><Context path="/myapp" allowLinking="true"></Context>' > context.xml |
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sudo mv context.xml /var/lib/tomcat6/webapps/PlasMapper/META-INF/ |
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sudo /etc/init.d/tomcat6 restart |
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# Here PlasMapper works on your server at the url http://myserver:8080/PlasMapper |
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Migration |
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cd /var/www/labstocks |
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sudo cp -r ../labstocks.bck2/plasmid_files/*.gb.gz plasmid_files/. |
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sudo chmod -R a+r plasmid_files |
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sudo chown -R www-data:www-data plasmid_files |
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sudo cp -r ../labstocks.bck2/collections collections/. |
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cd raw_dirs/antibodies/ |
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sudo mkdir `for ((a=1; a <= 24 ; a++)); do echo $a ; done` |
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cd ../.. |
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sudo cp ../labstocks.bck2/antibody_files/10.Anti-H3K14ac\(07-353\).pdf raw_dirs/antibodies/10/Anti-H3K14ac\(07-353\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/11.Anti-H3ac\(06-599\).pdf raw_dirs/antibodies/11/Anti-H3ac\(06-599\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/12.Anti-H3\(ab1791\).pdf raw_dirs/antibodies/12/Anti-H3\(ab1791\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/13.Anti-FLAG\(F7425\).pdf raw_dirs/antibodies/13/Anti-FLAG\(F7425\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/14.Cre-Recombinase\(PRB-106C\).pdf raw_dirs/antibodies/14/Cre-Recombinase\(PRB-106C\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/15.GAPDH-HRP\(ab85760\).pdf raw_dirs/antibodies/15/GAPDH-HRP\(ab85760\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/16.Anti-H3K9ac\(ab10812\).pdf raw_dirs/antibodies/16/Anti-H3K9ac\(ab10812\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/17.Anti-H3K4me3\(CS-003-100\).pdf raw_dirs/antibodies/17/Anti-H3K4me3\(CS-003-100\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/18.Anti-H3\(ab1791\).pdf raw_dirs/antibodies/18/Anti-H3\(ab1791\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/19.Anti-H3K4me1\(07-436\).pdf raw_dirs/antibodies/19/Anti-H3K4me1\(07-436\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/1.Anti-Actin-C4\(69100\).pdf raw_dirs/antibodies/1/Anti-Actin-C4\(69100\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/20.Anti-H3K14ac\(07-353\).pdf raw_dirs/antibodies/20/Anti-H3K14ac\(07-353\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/21.Anti-H4K12ac\(07-595\).pdf raw_dirs/antibodies/21/Anti-H4K12ac\(07-595\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/22.Anti-Htz1\(39647\).pdf raw_dirs/antibodies/22/Anti-Htz1\(39647\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/23.Anti-H2AFZ\(ab4626\).pdf raw_dirs/antibodies/23/Anti-H2AFZ\(ab4626\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/24.Anti-LexA-DBD\(39185\).pdf raw_dirs/antibodies/24/Anti-LexA-DBD\(39185\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/2.Anti-Myc\(06-340\).pdf raw_dirs/antibodies/2/Anti-Myc\(06-340\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/3.Anti-H3\(ab10799\).pdf raw_dirs/antibodies/3/Anti-H3\(ab10799\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/4.Anti-H3\(ab24834\).pdf raw_dirs/antibodies/4/Anti-H3\(ab24834\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/5.Anti-H3K4me2\(ab7766\).pdf raw_dirs/antibodies/5/Anti-H3K4me2\(ab7766\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/6.Anti-H3K4me3\(ab8580\).pdf raw_dirs/antibodies/6/Anti-H3K4me3\(ab8580\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/7.Anti-H3K27me3\(07-449\).pdf raw_dirs/antibodies/7/Anti-H3K27me3\(07-449\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/8.Anti-H4K12ac\(06-761\).pdf raw_dirs/antibodies/8/Anti-H4K12ac\(06-761\).pdf |
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sudo cp ../labstocks.bck2/antibody_files/9.Beta-Actin-AC74\(A2228\).pdf raw_dirs/antibodies/9/Beta-Actin-AC74\(A2228\).pdf |
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sudo chmod -R a+r raw_dirs |
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sudo chown -R www-data:www-data raw_dirs |
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# upload gene_synthesis_reports_pGY247.zip and gene_synthesis_reports_pGY248.zip |
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sudo chown root:www-data /var/lib/tomcat6/webapps/PlasMapper/dataBase/db_vectorFeature/*.* |
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sudo chmod 664 /var/lib/tomcat6/webapps/PlasMapper/dataBase/db_vectorFeature/*.* |
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sudo chown root:www-data /var/lib/tomcat6/webapps/PlasMapper/dataBase/db_vectorFeature/ |
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sudo chmod 775 /var/lib/tomcat6/webapps/PlasMapper/dataBase/db_vectorFeature/ |
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sudo chown root:www-data /var/lib/tomcat6/webapps/PlasMapper/html/feature.html |
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sudo chmod 664 /var/lib/tomcat6/webapps/PlasMapper/html/feature.html |
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# Here plasmids feature could be blasted by MyLabStock |
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cd ../../.. |
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Install MyLabStocks |
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------------------- |
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sudo cp -r mylabstocks/src /var/www/labstocks |
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sudo rm /var/www/labstocks/ |
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sudo touch /var/www/labstocks/formatdb.log |
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sudo chmod 440 /var/www/labstocks/connect_entry.php |
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sudo mkdir /var/www/labstocks/plasmid_files |
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sudo mkdir /var/www/labstocks/raw_dirs |
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sudo mkdir /var/www/labstocks/collections |
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sudo chown -R www-data:www-data /var/www/labstocks/connect_entry.php /var/www/labstocks/formatdb.log /var/www/labstocks/plasmid_files /var/www/labstocks/raw_dirs |
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scp -r stainer:Desktop/LBMC/projects/plasmapper/src/plasmid_files labstocks |
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vi labstocks/connect_entry.php |
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sudo cp -r labstocks /var/www/ |
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sudo chmod 440 /var/www/labstocks/connect_entry.php |
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sudo chown www-data:www-data /var/www/labstocks/connect_entry.php |
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sudo chown -R www-data:www-data /var/www/labstocks/plasmid_files |
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sudo chown -R www-data:www-data /var/www/labstocks/raw_dirs |
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sudo touch /var/www/labstocks/formatdb.log |
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sudo chown www-data:www-data /var/www/labstocks/formatdb.log |
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Configurate MyLabStocks |
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----------------------- |
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Now you have to update connexion params in |
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/var/www/labstocks/connect_entry.php |
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sudo vi /var/www/labstocks/connect_entry.php |
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finally run the following script to define passwords and instantiate |
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db. |
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php mylabstocks/src/install_db.phpsh |
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Congratulation your LabStocks instance is available on the url |
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http://your_server/labstocks. |
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Links |
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----- |
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*MyLabStocks* home, repository and documentation: http://forge.cbp |
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.ens-lyon.fr/redmine/projects/mylabstocks |
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Gael Yvert lab: http://www.ens-lyon.fr/LBMC/gisv/ |
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Usage |
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===== |
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In the strain section, the form `Search in genotype` filters strains where the |
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fields `locus1`, `locus2`, `locus3`, `locus4`, `locus5`, `ADE2`, `HIS3`, `LEU2`, |
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`LYS2`, `MET15`, `TRP1`, `URA3`, `HO_`, `Cytoplasmic_Character` or |
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`extrachromosomal_plasmid` contain the given expression. This filter is case |
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insensitive. |
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Even in edit mode, users are not granted permission to directly edit a plasmid |
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sequence, nor the URL to the plasmid sequence file. If a new sequence must be |
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entered instead of the current one, users must upload a new sequence file, in |
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.gb or .gb.gz format. MyLabStocks then automatically reads the file and update |
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the sequence field and the URL. This ensures consistency between URL, sequence |
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and the file itself. |
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TODO |
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==== |
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- Upload a .gb file, gzip it on fly for plasmids. |
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- Bug with plasmid 246, having a look on log file: tail -f /var/log/tomcat6/catalina.out |
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- Add persistence on advanced search form conditions. |
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- Remove file field for antibodies |
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- More error msg when an uploaded file is too big. (>2Mo). |
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Advanced Search |
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In the strain section, the form *Search in genotype* filters strains |
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where the fields *locus1*, *locus2*, *locus3*, *locus4*, *locus5*, |
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*ADE2*, *HIS3*, *LEU2*, *LYS2*, *MET15*, *TRP1*, *URA3*, *HO_*, |
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*Cytoplasmic_Character* or *extrachromosomal_plasmid* contain the |
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given expression. This filter is case insensitive. |
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Plasmids Sequences Management |
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Even in edit mode, users are not granted permission to directly edit a |
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plasmid sequence, nor the URL to the plasmid sequence file. If a new |
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sequence must be entered instead of the current one, users must upload |
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a new sequence file, in .gb or .gb.gz format. MyLabStocks then |
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automatically reads the file and update the sequence field and the |
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URL. This ensures consistency between URL, sequence and the file |
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itself. |
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Formats disponibles : Unified diff