LBMC » MyLabStocks

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Readme / Documentation for `MyLabStocks`

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`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.

.. code:: bash

  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.

.. code:: bash

  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.

.. code:: bash

  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 ../..

..

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.

.. code:: bash

  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.

.. code:: bash

  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

..

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

.. code:: bash

  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:

.. code:: bash

  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.

.. code:: bash

  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.

.. code:: bash

  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.