LBMC » MyLabStocks

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

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.

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.

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

=========================

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

-------------

Prior to installing MyLabStocks, a number of packages must be

installed on your system. Git is used to retrieve MyLabStocks sources.

MySQL, Apache and phpMyAdmin ensure web and database services, it

needs php5 and php5-curl packages. Tomcat6 will support advanced

plasmid visualisation services (PlasMapper), it needs openjdk-6-jdk

and ant. Finally, BLAST is used to analyse sequences, it needs csh.

On the targeted server, you can install these packages by typing the

following command in a terminal.

   sudo apt-get install git apache2 mysql-server php5 php5-curl phpmyadmin tomcat6 ant openjdk-6-jdk blast2 csh

Get MyLabStocks Sources

-----------------------

The first installation step is to retrieve the source code of

MyLabStocks. You can do this by typing the following command in a

terminal.

   git clone http://forge.cbp.ens-lyon.fr/git/mylabstocks

Install wwwBLAST

----------------

MyLabStocks uses BLAST queries for several of its features, wwwBLAST

is a web interface which provides access to this feature in a user-

friendly way.

MyLabStocks is distributed with wwwBLAST working on a x64

architecture. For other architectures, please refer to the NCBI

repositories http://mirrors.vbi.vt.edu/mirrors/ftp.ncbi.nih.gov/blast

/executables/release/LATEST

On the targeted server type the following commands in a terminal.

   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 "Alias /blast /var/www/blast/" > /tmp/blast.conf

   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

   sudo ln -s ../conf.d/blast.conf /etc/apache2/conf-available/blast.conf

   sudo ln -s ../conf-available/blast.conf /etc/apache2/conf-enabled/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 ../..

Now you have a wwwBLAST instance available here:

http://your_server/blast.

Install PlasMapper

------------------

PlasMapper provides advanced plasmid visualisation features. We use it

to produced annoted plasmid maps. To install it, type the following

command under a targeted server terminal.

   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

   # After these steps, 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

   # After these steps, PlasMapper works on your server at the url http://myserver:8080/PlasMapper

   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

   #  Now, plasmid features are ready to be searched by MyLabStocks via BLAST queries.

   cd ../../..

Now you have a PlasMapper instance available here:

http://your_server:8080/PlasMapper.

Install MyLabStocks

-------------------

Now your are ready to install the core of MyLabStocks. It consists of

a set of php scripts that you have to deploy on your apache server. To

do that, type the following commands in a targeted server terminal.

   sudo rsync -cauvz mylabstocks/src/ /var/www/labstocks/

   sudo rm /var/www/labstocks/install_db.phpsh

   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

   echo "Alias /blast /var/www/blast/" > /tmp/blast.conf

   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

   sudo ln -s ../conf.d/blast.conf /etc/apache2/conf-available/blast.conf

   sudo ln -s ../conf-available/blast.conf /etc/apache2/conf-enabled/blast.conf

   rm /tmp/blast.conf

Configure MyLabStocks

---------------------

For obvious security reasons, it is essential that you now update

connexion parameters by editing the script:

/var/www/labstocks/connect_entry.php

In this script you have to update the following constants:

   * SERVEUR

   * NOM

   * BASE

   * PASSE

   * LABNAME

   sudo vi /var/www/labstocks/connect_entry.php

We have prepared the following script to help you define passwords and

instantiate the database. This script will ask you to choose a

password for basic and administrative access. To use this script,

simply type the following command line:

   sudo php mylabstocks/src/install_db.phpsh

Congratulations! Your MyLabStocks instance is now available here:

http://your_server/labstocks.

Go to http://your_server/labstocks/wwwblast.php to initialize blast

databases.

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

=====

Advanced Search

---------------

In the strain section, the form *Search in genotype* filters strains

where the fields *locus1*, *locus2*, *locus3*, *locus4*, *locus5*,

*ADE2*, *HIS3*, *LE  U2*, *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.

Reporting Bugs

--------------

If you think you have found a bug and would like to report the

problem, then please ensure you have applied all applicable updates.

If this is the case, send a description of your problem and some

screenshot to florent.chuffart on its ens-lyon.fr email. Thank you for

your contribution.

Backing up the Mysql Database and Stored Files

----------------------------------------------

We HIGHLY RECOMMEND THAT YOU REGULARLY BACKUP your MyLabStocks

database. We provide two levels of backup. The first one dumps only

the MySQL database. The second one also adds the items' files that

were uploaded on the server (plasmid_files and raw_dirs directories

from your /var/www/labstocks directory). These two features are

available on the bottom of each entry page. The two links in the

sentence *Backup the entire system or only the database NOW!* allow

any user to download the requested backups. It could be useful for an

administrator to integrate it in a robust file backup system using,

for example, a cron that regularly pull the archives (wget

http://.../labstocks/backup.php?FULL_BACK=1). A third link allow you

to export the current table in ''csv'' format.

How To Restore System From Backup

---------------------------------

On the targeted server, you can restore the database from the last

backup file ''labstocks_db.sql'' by typing the following command in a

terminal. Not that you need administrator priviledges on the server to

do that. This will drop existing tables, create new ones and populate

them with data. You need to adapt user, password and database names

according to your settings.

   sudo mysql --user=root --password=root labstocks_db < labstocks_db.sql

To restore the uploaded files, you have to copy backed-up directories

(''plasmid_files'' and ''raw_dirs'') to the labstocks directory of

your server. To do that, on the targeted server, type the following

commands in a terminal.

   sudo cp -r plasmid_files raw_dirs /var/www/labstocks/.

Extend Database

---------------

MyLabstocks is delivered under a free licence. Feel free to modify and

extend it to meet the needs of your lab. To do that you can create new

tables using phpMyAdmin (http://your_server/phpmyadmin) or mysql

command line tools (documentation here

http://dev.mysql.com/doc/refman/5.6/en/mysql.html). MyLabStocks uses

the  framework phpMyEdit to manage the user interface. You can use the

provided tool (http://your_server/phpMyEditSetup.php) to generate

code. You can learn how to customize the interface by reading the

phpMyEdit embedded documentation

(http://your_server/labstocks/doc/html/).

Adding New Boxes In The Box Manager

-----------------------------------

Tu add new boxes in the box manager you have to connect to the box

manager in super user mode (or asking to your admin to). In this

contexte, at the top of the page appears a link ''Add a new box for

your Liquid N2 storage''. Follow this link, fill the form and click

the button ''Add this new box''.

Modifying The Session Duration

------------------------------

To modify the session duration, edit the connect_entry.php

configuration file and modify the SESSION_DURATION default value.

Extracting the genotypes of multiple strains when preparing a publication

-------------------------------------------------------------------------

Log in with superuser priviledges. Go to the strains tab, click on the

'extract genotypes' link above the table Enter IDs of strains to be

retrieved, separated by blank space or commas. Click on 'extract

genotypes' button.

Clearing Existing Values and Start Over

---------------------------------------

Existing values can be deleted from the admin tab using the superuser

password. By doing so, you have to take care of the order in which you

delete entries. For example, your are allowed to delete an "author"

only if this author is no longer associated with any item entry

("strain", "lab book", ...). It is therefore necessary to first delete

these item entries befor this author. Existing entries can also be

deleted via SQL requests or through the phpMyAdmin graphical

interface, using the DUMP TABLE command.