commit f78441a46962ba61f8167f76bfecfcdc25ec90de
Author: Florent Chuffart <florent.chuffart@ens-lyon.fr>
Date:   Thu Oct 24 11:41:56 2013 +0200

    Fixing doc.

diff --git a/README b/README
index 2a65019..213ac9f 100644
--- a/README
+++ b/README
@@ -1,154 +1,221 @@
-*****************************************
-Readme / Documentation for `MyLabsStocks`
-*****************************************
 
-`MyLabsStocks` offers Python API and R package allowing to perform 
-quantitative analysis of nucleosomal epigenome. It is especially well 
-suited for scripting to extract natural Single-Nucleosome Epi-
-Polymorphisms (SNEP) from ChIP-Seq data.
+Readme / Documentation for *MyLabStocks*
+****************************************
+
+*MyLabStocks* is a web application allowing to easily store, share and
+retrieve information about molecular biology materials stored in a
+laboratory.
+
 
 License
 =======
 
-Copyright CNRS 2012-2013                                                 
-                                                                          
-- Florent CHUFFART                                                         
-- Gael YVERT                                                               
-                                                                          
-This software is a computer program which purpose is to perform quanti-
-tative analysis of epigenetic marks at single nucleosome resolution.     
-                                                                          
-The Software is provided “as is” without warranty of any kind, either 
-express or implied, including without lim- itation any implied warranties 
-of condition, uninterrupted use, merchantability, fitness for a particular 
-purpose, or non-infringement. You use this software at your own risk.
-
-This software is governed by the CeCILL license under French law and     
-abiding by the rules of distribution of free software.  You can  use,    
-modify and/ or redistribute the software under the terms of the CeCILL   
-license as circulated by CEA, CNRS and INRIA at the following URL        
-"http://www.cecill.info".                                                
-                                                                          
-As a counterpart to the access to the source code and  rights to copy,   
-modify and redistribute granted by the license, users are provided only  
-with a limited warranty  and the software's author,  the holder of the   
-economic rights,  and the successive licensors  have only  limited       
-liability.                                                               
-                                                                          
-In this respect, the user's attention is drawn to the risks associated   
-with loading,  using,  modifying and/or developing or reproducing the    
-software by the user in light of its specific status of free software,   
-that may mean  that it is complicated to manipulate,  and  that  also    
-therefore means  that it is reserved for developers  and  experienced    
-professionals having in-depth computer knowledge. Users are therefore    
-encouraged to load and test the software's suitability as regards their  
-requirements in conditions enabling the security of their systems and/or 
-data to be ensured and,  more generally, to use and operate it in the    
-same conditions as regards security.                                     
-                                                                          
-The fact that you are presently reading this means that you have had     
-knowledge of the CeCILL license and that you accept its terms.           
+Copyright CNRS 2012-2013
+
+* Florent CHUFFART
+
+* Gael YVERT
+
+This software is a computer program which purpose is to perform
+quantitative analysis of epigenetic marks at single nucleosome
+resolution.
+
+The Software is provided “as is” without warranty of any kind, either
+express or implied, including without limitation any implied
+warranties of condition, uninterrupted use, merchantability, fitness
+for a particular purpose, or non-infringement. You use this software
+at your own risk.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software.  You can  use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and  rights to copy,
+modify and redistribute granted by the license, users are provided
+only  with a limited warranty  and the software's author,  the holder
+of the economic rights,  and the successive licensors  have only
+limited liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading,  using,  modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean  that it is complicated to manipulate,  and  that  also
+therefore means  that it is reserved for developers  and  experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards
+their requirements in conditions enabling the security of their
+systems and/or data to be ensured and,  more generally, to use and
+operate it in the same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+
 
 Installation Instructions
 =========================
 
-Links
------
+This installation has been fully tested on:
+   * Debian 7.2.0 amd64 netinst [1], running on virtual machine using
+     Oracle VM VirtualBox [2] for macosx (dev)
+
+   * Ubuntu Server 12.04.3 LTSUbuntu server LTS [3], running on
+     physical machine (prod)
+
+[1] http://cdimage.debian.org/debian-cd/7.2.0/amd64/iso-
+cd/debian-7.2.0-amd64-netinst.iso
+
+[2] https://www.virtualbox.org
+
+[3] http://www.ubuntu.com/download/server
+
+
+Prerequisites
+-------------
+
+   sudo apt-get install git mysql-server apache2 php5 phpmyadmin php5-curl csh blast2 tomcat ant openjdk-6-jdk
+
+
+Get MyLabStocks Sources
+-----------------------
+
+   git clone http://forge.cbp.ens-lyon.fr/git/mylabstocks
 
-`MyLabsStocks` home page: http://www.ens-lyon.fr/LBMC/gisv/
 
-`MyLabsStocks` documentation: http://www.ens-lyon.fr/LBMC/gisv/
+Install wwwBlast
+----------------
+
+MyLabStocks is distributed with wwwblast working on a x64
+architecture. For other architectures refer to the NCBI repositories h
+ttp://mirrors.vbi.vt.edu/mirrors/ftp.ncbi.nih.gov/blast/executables/re
+lease/LATEST
 
+   cd mylabstocks/opts/
+   tar xfvz wwwblast-2.2.26-x64-linux.tar.gz
+   sudo cp -r blast /var/www/.
+   sudo chown www-data:www-data /var/www/blast/TmpGifs /var/www/blast/*.log /var/www/blast/db/
+   echo "<Directory /var/www/blast/>" > /tmp/blast.conf
+   echo "   Options +ExecCGI" >> /tmp/blast.conf
+   echo "</Directory>" >> /tmp/blast.conf
+   echo "AddHandler cgi-script .cgi" >> /tmp/blast.conf
+   sudo cp /tmp/blast.conf /etc/apache2/conf.d/blast.conf
+   rm /tmp/blast.conf
+   sudo /etc/init.d/apache2 restart
+   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
+   sudo sed -i 's/<option VALUE.*test_aa_db//g' /var/www/blast/blast.html
+   cat /var/www/blast/blast.rc > /tmp/blast.rc
+   echo "blastn oligostock_db" >> /tmp/blast.rc
+   echo "tblastn oligostock_db" >> /tmp/blast.rc
+   echo "tblastx oligostock_db" >> /tmp/blast.rc
+   echo "blastn plasmidstock_db" >> /tmp/blast.rc
+   echo "tblastn plasmidstock_db" >> /tmp/blast.rc
+   echo "tblastx plasmidstock_db" >> /tmp/blast.rc
+   echo "blastn plfeatstock_db" >> /tmp/blast.rc
+   echo "tblastn plfeatstock_db" >> /tmp/blast.rc
+   echo "tblastx plfeatstock_db" >> /tmp/blast.rc
+   sudo cp /tmp/blast.rc /var/www/blast/blast.rc
+   rm /tmp/blast.rc
+   cd ../..
 
-Installation
-------------
 
-rsync -cauvz  --exclude="formatdb.log" --exclude=".DS_Store" ../src/ root@cremone:/var/www/labstocks/
+Install PlasMapper
+------------------
 
-cd /var/www/labstocks
-# sudo vi connect_entry.php 
-sudo touch formatdb.log
-sudo chmod 440 connect_entry.php 
-sudo chown -R www-data:www-data connect_entry.php formatdb.log  plasmid_files raw_dirs
+   cd mylabstocks/opts/
+   tar xfvz PlasMapper_download.tar.gz
+   cd PlasMapper
+   # modify installdir as /var/lib/tomcat6
+   sed -i 's/\/home\/tomcat/\/var\/lib\/tomcat6/g' build.xml
+   # modify servletjar as /usr/share/tomcat6/lib/servlet-api.jar
+   sed -i 's/${installdir}\/common\/lib\/servlet-api.jar/\/usr\/share\/tomcat6\/lib\/servlet-api.jar/g' build.xml
+   # change /home/tomcat for /var/lib/tomcat6
+   sed -i 's/\/home\/tomcat/\/var\/lib\/tomcat6/g' src/ca/ualberta/xdong/plasMapper/annotate/plasMapConfiguration_en_CA.properties
+   # and set blastallDir=/usr/bin/
+   sed -i 's/\/usr\/local\/bin\//\/usr\/bin\//g' src/ca/ualberta/xdong/plasMapper/annotate/plasMapConfiguration_en_CA.properties
+   # Here PlasMapper is ready to be configured
 
+   ant clean
+   ant build
+   sudo ant install
+   sudo rm -Rf /var/lib/tomcat6/webapps/PlasMapper/tmp
+   sudo ln -s /tmp/tomcat6-tomcat6-tmp/ /var/lib/tomcat6/webapps/PlasMapper/tmp
+   echo '<?xml version="1.0" encoding="UTF-8"?><Context path="/myapp" allowLinking="true"></Context>' > context.xml
+   sudo mv context.xml /var/lib/tomcat6/webapps/PlasMapper/META-INF/
+   sudo /etc/init.d/tomcat6 restart
+   # Here PlasMapper works on your server at the url http://myserver:8080/PlasMapper
 
-Migration
-cd /var/www/labstocks
-sudo cp -r ../labstocks.bck2/plasmid_files/*.gb.gz plasmid_files/.
-sudo chmod -R a+r plasmid_files
-sudo chown -R www-data:www-data plasmid_files
-sudo cp -r ../labstocks.bck2/collections collections/.
-cd raw_dirs/antibodies/
-sudo mkdir `for ((a=1; a <= 24 ; a++)); do echo $a ; done`
-cd ../..
-sudo cp ../labstocks.bck2/antibody_files/10.Anti-H3K14ac\(07-353\).pdf                raw_dirs/antibodies/10/Anti-H3K14ac\(07-353\).pdf                            
-sudo cp ../labstocks.bck2/antibody_files/11.Anti-H3ac\(06-599\).pdf                   raw_dirs/antibodies/11/Anti-H3ac\(06-599\).pdf                               
-sudo cp ../labstocks.bck2/antibody_files/12.Anti-H3\(ab1791\).pdf                     raw_dirs/antibodies/12/Anti-H3\(ab1791\).pdf                                 
-sudo cp ../labstocks.bck2/antibody_files/13.Anti-FLAG\(F7425\).pdf                    raw_dirs/antibodies/13/Anti-FLAG\(F7425\).pdf                                
-sudo cp ../labstocks.bck2/antibody_files/14.Cre-Recombinase\(PRB-106C\).pdf           raw_dirs/antibodies/14/Cre-Recombinase\(PRB-106C\).pdf                        
-sudo cp ../labstocks.bck2/antibody_files/15.GAPDH-HRP\(ab85760\).pdf                  raw_dirs/antibodies/15/GAPDH-HRP\(ab85760\).pdf                              
-sudo cp ../labstocks.bck2/antibody_files/16.Anti-H3K9ac\(ab10812\).pdf                raw_dirs/antibodies/16/Anti-H3K9ac\(ab10812\).pdf                            
-sudo cp ../labstocks.bck2/antibody_files/17.Anti-H3K4me3\(CS-003-100\).pdf            raw_dirs/antibodies/17/Anti-H3K4me3\(CS-003-100\).pdf                         
-sudo cp ../labstocks.bck2/antibody_files/18.Anti-H3\(ab1791\).pdf                     raw_dirs/antibodies/18/Anti-H3\(ab1791\).pdf                                 
-sudo cp ../labstocks.bck2/antibody_files/19.Anti-H3K4me1\(07-436\).pdf                raw_dirs/antibodies/19/Anti-H3K4me1\(07-436\).pdf                            
-sudo cp ../labstocks.bck2/antibody_files/1.Anti-Actin-C4\(69100\).pdf                 raw_dirs/antibodies/1/Anti-Actin-C4\(69100\).pdf                             
-sudo cp ../labstocks.bck2/antibody_files/20.Anti-H3K14ac\(07-353\).pdf                raw_dirs/antibodies/20/Anti-H3K14ac\(07-353\).pdf                            
-sudo cp ../labstocks.bck2/antibody_files/21.Anti-H4K12ac\(07-595\).pdf                raw_dirs/antibodies/21/Anti-H4K12ac\(07-595\).pdf                            
-sudo cp ../labstocks.bck2/antibody_files/22.Anti-Htz1\(39647\).pdf                    raw_dirs/antibodies/22/Anti-Htz1\(39647\).pdf                                
-sudo cp ../labstocks.bck2/antibody_files/23.Anti-H2AFZ\(ab4626\).pdf                  raw_dirs/antibodies/23/Anti-H2AFZ\(ab4626\).pdf                              
-sudo cp ../labstocks.bck2/antibody_files/24.Anti-LexA-DBD\(39185\).pdf                raw_dirs/antibodies/24/Anti-LexA-DBD\(39185\).pdf                            
-sudo cp ../labstocks.bck2/antibody_files/2.Anti-Myc\(06-340\).pdf                     raw_dirs/antibodies/2/Anti-Myc\(06-340\).pdf                                 
-sudo cp ../labstocks.bck2/antibody_files/3.Anti-H3\(ab10799\).pdf                     raw_dirs/antibodies/3/Anti-H3\(ab10799\).pdf                                 
-sudo cp ../labstocks.bck2/antibody_files/4.Anti-H3\(ab24834\).pdf                     raw_dirs/antibodies/4/Anti-H3\(ab24834\).pdf                                 
-sudo cp ../labstocks.bck2/antibody_files/5.Anti-H3K4me2\(ab7766\).pdf                 raw_dirs/antibodies/5/Anti-H3K4me2\(ab7766\).pdf                             
-sudo cp ../labstocks.bck2/antibody_files/6.Anti-H3K4me3\(ab8580\).pdf                 raw_dirs/antibodies/6/Anti-H3K4me3\(ab8580\).pdf                             
-sudo cp ../labstocks.bck2/antibody_files/7.Anti-H3K27me3\(07-449\).pdf                raw_dirs/antibodies/7/Anti-H3K27me3\(07-449\).pdf                            
-sudo cp ../labstocks.bck2/antibody_files/8.Anti-H4K12ac\(06-761\).pdf                 raw_dirs/antibodies/8/Anti-H4K12ac\(06-761\).pdf                             
-sudo cp ../labstocks.bck2/antibody_files/9.Beta-Actin-AC74\(A2228\).pdf               raw_dirs/antibodies/9/Beta-Actin-AC74\(A2228\).pdf                           
-sudo chmod -R a+r raw_dirs
-sudo chown -R www-data:www-data raw_dirs
-# upload gene_synthesis_reports_pGY247.zip and gene_synthesis_reports_pGY248.zip
+   sudo chown root:www-data /var/lib/tomcat6/webapps/PlasMapper/dataBase/db_vectorFeature/*.*
+   sudo chmod 664 /var/lib/tomcat6/webapps/PlasMapper/dataBase/db_vectorFeature/*.*
+   sudo chown root:www-data /var/lib/tomcat6/webapps/PlasMapper/dataBase/db_vectorFeature/
+   sudo chmod 775 /var/lib/tomcat6/webapps/PlasMapper/dataBase/db_vectorFeature/
+   sudo chown root:www-data /var/lib/tomcat6/webapps/PlasMapper/html/feature.html
+   sudo chmod 664 /var/lib/tomcat6/webapps/PlasMapper/html/feature.html
+   # Here plasmids feature could be blasted by MyLabStock
 
+   cd ../../..
 
 
+Install MyLabStocks
+-------------------
 
+   sudo cp -r mylabstocks/src /var/www/labstocks
+   sudo rm /var/www/labstocks/
+   sudo touch /var/www/labstocks/formatdb.log
+   sudo chmod 440 /var/www/labstocks/connect_entry.php
+   sudo mkdir /var/www/labstocks/plasmid_files
+   sudo mkdir /var/www/labstocks/raw_dirs
+   sudo mkdir /var/www/labstocks/collections
+   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
 
-scp -r stainer:Desktop/LBMC/projects/plasmapper/src/plasmid_files labstocks
-vi labstocks/connect_entry.php
-sudo cp -r labstocks /var/www/
-sudo chmod 440 /var/www/labstocks/connect_entry.php 
-sudo chown www-data:www-data /var/www/labstocks/connect_entry.php
-sudo chown -R www-data:www-data /var/www/labstocks/plasmid_files
-sudo chown -R www-data:www-data /var/www/labstocks/raw_dirs
-sudo touch /var/www/labstocks/formatdb.log
-sudo chown www-data:www-data /var/www/labstocks/formatdb.log
+
+Configurate MyLabStocks
+-----------------------
+
+Now you have to update connexion params in
+/var/www/labstocks/connect_entry.php
+
+   sudo vi /var/www/labstocks/connect_entry.php
+
+finally run the following script to  define passwords and instantiate
+db.
+
+   php mylabstocks/src/install_db.phpsh
+
+Congratulation your LabStocks instance is available on the url
+http://your_server/labstocks.
 
 
+Links
+-----
 
+*MyLabStocks* home, repository and documentation: http://forge.cbp
+.ens-lyon.fr/redmine/projects/mylabstocks
 
+Gael Yvert lab: http://www.ens-lyon.fr/LBMC/gisv/
 
 
 Usage
 =====
 
-In the strain section, the form `Search in genotype` filters strains where the 
-fields `locus1`, `locus2`, `locus3`, `locus4`, `locus5`, `ADE2`, `HIS3`, `LEU2`, 
-`LYS2`, `MET15`, `TRP1`, `URA3`, `HO_`, `Cytoplasmic_Character` or 
-`extrachromosomal_plasmid` contain the given expression. This filter is case 
-insensitive.
-
-Even in edit mode, users are not granted permission to directly edit a plasmid 
-sequence, nor the URL to the plasmid sequence file. If a new sequence must be 
-entered instead of the current one, users must upload a new sequence file, in 
-.gb or .gb.gz format. MyLabStocks then automatically reads the file and update 
-the sequence field and the URL. This ensures consistency between URL, sequence 
-and the file itself.
-
-TODO
-====
-
-  - Upload a .gb file, gzip it on fly for plasmids.
-  - Bug with plasmid 246, having a look on log file: tail -f /var/log/tomcat6/catalina.out
-  - Add persistence on advanced search form conditions.
-  - Remove file field for antibodies
-  - More error msg when an uploaded file is too big. (>2Mo).
\ No newline at end of file
+
+Advanced Search
+---------------
+
+In the strain section, the form *Search in genotype* filters strains
+where the fields *locus1*, *locus2*, *locus3*, *locus4*, *locus5*,
+*ADE2*, *HIS3*, *LEU2*, *LYS2*, *MET15*, *TRP1*, *URA3*, *HO_*,
+*Cytoplasmic_Character* or *extrachromosomal_plasmid* contain the
+given expression. This filter is case insensitive.
+
+
+Plasmids Sequences Management
+-----------------------------
+
+Even in edit mode, users are not granted permission to directly edit a
+plasmid sequence, nor the URL to the plasmid sequence file. If a new
+sequence must be entered instead of the current one, users must upload
+a new sequence file, in .gb or .gb.gz format. MyLabStocks then
+automatically reads the file and update the sequence field and the
+URL. This ensures consistency between URL, sequence and the file
+itself.
