Download and Install TUIT

Shestopalov Lab

TUIT installation guide

PLEASE NOTE, THAT STARTING VERSION 1.0, TUIT HAS AN OPTION TO KEEP THE TAXONOMIC DATABASE IN RAM INSTEAD OF THE RDBMS (MySQL). TO USE THE LEGACY VERSION - USE THE -usedb OPTION AT THE END OF THE COMMAND LINE. THE PART OF THE INSTALLATION PROCEDURE IS NOT REQUIRED IF YOU ARE NOT PLANNING TO USE THE RDBMS.


The process will require ~7GB of free HDD space, most of which may be freed up after the installation has finished.



The installation procedure consists of 3 main parts:



1. Preparing the environment



2. Downloading a copy of TUIT executable



3. Deploying the taxonomic database from the NCBI taxonomic data



1. In order to successfully operate, TUIT module needs the following prerequisites fulfilled:




  • Java 7 SE installed


  • MySQL installed locally or on a remote server


  • BLASTN executable from the NCBI



· (
Optional) NT database from the NCBI deployed locally (please refer to the NCBI official manual ftp://ftp.ncbi.nlm.nih.gov/blast/documents/blastdb.html for more information on this
point



· A temporary folder for TUIT temporary files must also exist



Linux installation (apply if any of the components are missing)



1. Depending on the Linux distribution that you may be using, the installation process may vary. The easiest way would be to download Java7 .rpm package and install it as follows:



Java 7 SE can be downloaded for free form the Oracle web page

http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html



Click on the link above, select 32 or 64 bits Linux distribution from the bottom of the list, and click download



Follow the installation instructions. Additional instructions can be found by following the links below




2. MySQL is a free open source database, which can be downloaded form http://dev.mysql.com/downloads/mysql/ , however, almost every standard distro most likely already has
it preinstalled. Check if you already have MySQL: open terminal and type



$:> mysql --help



A help printout should appear. If not, install MySQL following the instructions, specific to your distro:




Having chosen the appropriate manual, install MySQL and create the password for the root (superuser).



3. Find, download and install a 32 or 64 bits version of BLAST depending on your system.



http://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/



NOTE
that you are going to use only the blastn executable.



4. Create a temporary directory in a preferred place on the file system and ensure that the directory is writable/readable (chmod 777) for all processes





Windows (apply if any of the components are missing)



1. Java 7 SE can be downloaded for free form the Oracle web page

http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html



Click on the link above, select 32 or 64 bits Windows distribution from the bottom of the list, and click download



Follow the installation instructions. Additional instructions may be found in the official manual http://www.java.com/en/download/help/windows_manual_download.xml



2. MySQL is a free open source database, which can be downloaded from http://dev.mysql.com/downloads/installer/ . Please NOTE that windows installation
also requires .NET framework preinstalled. If the MySQL installation complains about the missing .NET, follow this link and install .NET on your system http://www.microsoft.com/en-us/download/details.aspx?id=17113



Click the link above, choose a 32 or 64 bits copy from the list on the download page of the installation package and download. Install MySQL and create the
password for the root (superuser). Additional installation guides, common for all Windows versions, may be found in this educating videohttp://www.youtube.com/watch?v=AqQc3YqfelE and in the official documentation http://dev.mysql.com/doc/refman/5.1/en/windows-using-installer.html



3. Find, download and install a 32 or 64 bits version of BLAST depending on your system.



http://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/



NOTE
that as long as you only need the blastn executable, you do not require to install the full BLAST package, so it may be a good idea to download
only the ncbi-blast-2.2.28+-x64-win64.tar.gz archive and extract it to a temporary folder, pick the blastn.exe from the bin/ subfolder, save it
and delete the rest if you are not planning to use it



4. Create a temporary directory in a preferred place on the file system and ensure that the directory is writable/readable for all processes ( Please NOTE that some antivirus software may interfere with the folder being accessible from the MySQL)



MacOSX



1. Java 7 SE can be downloaded for free form the Oracle web page

http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html



Click on the link above, select Mac OS X x64 package, download and open. Follow the installation instructions. Additional instructions may be found in the
official manual http://docs.oracle.com/javase/7/docs/webnotes/install/mac/mac-jdk.html



2. MySQL is a free open source database, which can be downloaded form http://dev.mysql.com/downloads/mysql/



Click the link above, choose a 32 or 64 bits copy from the list on the download page of the installation package and download. Install MySQL and create the
password for the root (superuser). Additional installation guides, common for MacOSX, may be found in the official documentation http://dev.mysql.com/doc/refman/5.1/en/macosx-installation.html



3. Find, download the version of BLAST from the link below



http://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/



NOTE
that as long as you only need the blastn executable, you do not require to install the full BLAST package, so it may be a good idea to download
only the ncbi-blast-2.2.28+-universal-macosx.tar.gz archive and extract it to a temporary folder, pick the blastn executable file from the bin/
subfolder, save it and delete the rest if you are not planning to use it



4. Create a temporary directory in a preferred place on the file system and ensure that the directory is writable/readable for all processes



2. Download and setup TUIT module and the taxonomic database






1. Download the tuit.tar.gz from https://sourceforge.net/projects/tuit/files/. The archive contains



a. A precompiled tuit module, which contains tuit.jar executable and dependency libraries



b. An SQL script file (schema.sql) that deploys the taxonomic database schema and creates the “tuit@localhost” user that possesses rights to operate upon
the schema



c. A configuration file (properties.xml), which contains the commented parameters fields, which TUIT reads and uses at run



d. A MySQL Workbench file (NCBI Taxonomy.mwb), that describes the NCBI Taxonomic schema. MySQL Workbench is a free software tool that can be downloaded
from http://www.mysql.com/products/workbench/



2. Deploy TUIT as follows:



On Linux



1. Move tuit folder to /opt/tuit (or choose a different folder)



2. Move properties.xml to the same folder



(you may decide to create an alias



$:> alias tuit=’java -jar /opt/tuit.jar’



and make the alias permanent)



On Windows



1. Move tuit folder to C:\Program Files\tuit (or choose a different folder)



2. Move properties.xml to the same folder



On MacOSX



1. Move tuit folder to Applications/tuit (or choose a different folder)



2. Move properties.xml to the same folder






3. Deploy the taxonomic database from the NCBI ftp sever



The process is fully automated and is performed with the TUIT module. The user’s actions are limited to deploying the taxonomic schema within MySQL.



To do so, login to MySQL as superuser and use the schema.sql from the tuit archive as a source:



On Linux and MacOSX



1.
$:>mysql -u root -p



and enter password



2.
mysql:>source {path to }/schema.sql



3. You may now quit from MySQL






On Windows



1. Open MySQL Command Line Client terminal and log in as superuser



2.
mysql:>source {path to }/schema.sql



(remember that on windows you need to use “\” instead of “/” as a system paths separator)



3. You may now close the Command Line Client Window



The SQL script will format the necessary tables and create a “tuit@localhost” user, authorized to operate upon the NCBI schema. Now that the database is
set, you can run tuit module in “deploy” mode.



open terminal (CMD.exe on Windows) and type:



$:>java -jar {path to}/tuit.jar -p {path to}/properties.xml -deploy



if you did not change the <DBConnection url="localhost" login="tuit" password="tuit"/>



tag parameters in the properties.xml, tuit should be able to connect to the database



Depending on the speed of your system and internet connection, the initial process of the taxonomic database installation may take as long as several
hours. Further updates on the database should be much less time consuming. To update the database simply use the same command as above, but with “-update”
flag:



java -jar {path to}/tuit.jar -p {path to}/properties.xml -update


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