Installation
Outline
Here we explain commands of TASUKE for installation and making database. The time for creation of databases depends on genome size, number of samples and the power of server computer. Steps 5 and 7 are repeated for each accession.
We prepared a shell script as unified tool for installation. It automatically finds the files from specified directory and conducts these process. (it does not support GWAS and System phylogenetic tree.)
More detail: Unified installer

TASUKE browser requires the LAMP server. And it requires the Linux server that has Apache, MySQL5.0 to 5.2 with mysqli module, 5.3 or later and PHP5.0 or later.
At first you have to install php-mysql and modify httpd.conf(or php.conf) file as shown below.
If php-mysql is not installed, install it. If the result of the command "php -m" contains "mysqli", it is installed.$ yum install php-mysql
•CentOS php5.5 or later
$ yum install php-mysqlnd
•Ubuntu
$ apt install php-mysql
Set to run php in the .html file.
For CentOS, add or modifying '/etc/httpd/conf.d/php.conf'AddHandler php5-script .php AddHandler php5-script .php .html
•using php7.x
AddHandler php7-script .php AddHandler php7-script .php .html
SetHandler application/x-httpd-php
</FilesMatch>
Add or modifying '/etc/httpd/conf/httpd.conf'
...
AddType application/x-httpd-php .php .html
...
</IfModule>
LoadModule mpm_event_module modules/mod_mpm_event.so
LoadModule mpm_prefork_module modules/mod_mpm_prefork.so
#LoadModule mpm_event_module modules/mod_mpm_event.so
There may be other compatibility issues between PHP and MySQL.
If php-json is not installed(you're using php5.1(or earlier) or php7.x), please install it. If the result of the command "php -m" contains "json", it is installed.
e.g.) If you want to install curl module on Ubuntu PHP7.4.
If you want to upgrade from legacy TASUKE to TASUKE+, update your database schema as follows:
$ tasuke_update_for_gwas.pl -db <database name>
-u <user>
-p <password>
<database name>
: Database name for TASUKE-u
<user>
: User name-p
<password>
: Password for the databaseHere you create a MySQL database. First, you log-in to mysql with root authority and create a database. "database name" used here is used following installation steps.
$ mysql -u <user>
-p
> Enter password: <password>
$ mysql> create database <database name>
;
$ mysql> exit;
$ tasuke_update_for_gwas.pl -db <database name>
-u <user>
-p <password>
<database name>
: Database name for TASUKE-u
<user>
: User name-p
<password>
: Password for the databaseThis tool creates several tables on your database for TASUKE.
$ tasuke_init.pl -db <database name>
-u <user>
-p <password>
Required:
-db <database name>
: Database name for TASUKE
-u <user>
: User name
-p <password>
: Password for the database
Optional:
-h <remote host>
: To connect remote host name
-r : Delete the tables from database.
> Input csv file about chromosome's information below.
> Where is the csv file? > <information of reference genome(.csv)>
> Are you sure creating database [y|n] > y
$autoDetectSerialTable = 0;
When you missed in chromosome or accession list, you must create MySQL database again.
$ mysql -u <user>
-p
> Enter password: <your password>
$ mysql> drop database <database name>
;
$ mysql> create database <database name>
;
$ mysql> exit;
This tool registers the accessions to database.
$ tasuke_accession.pl -db <database name>
-u <user>
-p <password>
Required:
-db <database name>
: Database name for TASUKE
-u <user>
: User name
-p <password>
: Password for the database
Optional:
-h <remote host>
: To connect remote host name
-r : Delete the accessions from database.
> Input csv file about list of accessions below.
> Where is the csv file? > <accession list(.csv)>
:
> Are you sure adding or updating database?[y|n] > y
$ tasuke_accession.pl -r -db <database name>
-u <user>
-p <password>
-----------------------------------
Deleting accession from database
-----------------------------------
Input csv file about list of accessions below.
* WARNING : This process deletes not only accession information but also depth and variant data.
This tool sets reference genome to database.
$ tasuke_ref.pl -db <database name>
-u <user>
-p <password>
-f <reference genome>
Required:
-db <database name>
: Database name for TASUKE
-u <user>
: User name
-p <password>
: Password for the database
-f <reference genome>
: FASTA formatted reference genome file
Optional:
-h <remote host>
: To connect remote host name
-r : Delete the reference genome from database.
$ tasuke_ref.pl -r -db <database name>
-u <user>
-p <password>
This tool sets variants to database.
$ tasuke_variant_vcf.pl -db <database name>
-u <user>
-p <password>
-n <ID>
-f <variant file>
-t 'samtools' or 'freebayes' or 'gatk' or 'gatkm'
Required:
-db <database name>
: Database name for TASUKE
-u <user>
: User name
-p <password>
: Password for the database
-n <ID>
: Destination ID (accession)
-f <variant file>
: Variant infromation (.VCF)
-t 'samtools' or 'gatk' or 'gatkm' : Set the program name that generated VCF file to this section
'gatkm' means multi sample VCF file generated by GATK.
Optional:
-z : For "-t gatkm". Register GT:0/0 variant(not by default)
-h <remote host>
: To connect remote host name
-r : Delete the variants from database.
"gatkm" VCF file contains a GT:0/0 variant, but it is not registered in DB by default as it will increase data size and reduce performance. Add '-z' option to register GT:0/0 variant. GT:0/0 variant will be displayed on the track in GT color mode.
When you want to input a VCF file again, you can delete it with '-r' option.
$ tasuke_variant_vcf.pl -r -db <database name>
-u <user>
-p <password>
-n <ID>
This tool sets depth information to database. First you need to create TSV files from your BAMs (see Preparation section).
$ tasuke_tsv_db.pl -db <database name>
-u <user>
-p <password>
-n <ID>
-f <depth file>
Required:
-db <database name>
: Database name for TASUKE
-u <user>
: User name
-p <password>
: Password for the database
-n <ID>
: Destination ID (accession)
-f <Depth file>
: TSV formatted depth information file
Optional:
-h <remote host>
: To connect remote host name
-r : Delete the variants from database.
$ tasuke_tsv_db.pl -r -db <database name>
-u <user>
-p <password>
-n <ID>
This tool sets depth information to database. First you need to create TSV files from your BAMs (see Preparation section).
This tool inputs any kind of TSV formatted NGS data. To input the general purpose track, you can do it by using tasuke_tsv_db.pl with '-c' option. First you need to create TSV files from your BED or BEDgraph files (see Preparation section).
$ tasuke_tsv_db.pl -c -db <database name>
-u <user>
-p <password>
-n <ID>
-f <tsv file>
$ tasuke_tsv_db.pl -r -c -db <database name>
-u <user>
-p <password>
-n <ID>
If you want to set any multiple conditions to the general purpose track, try following command. And load a TSV file using tasuke_tsv_db.pl.
$ tasuke_add_condition.pl -db <database name>
-u <user>
-p <password>
-n <ID>
-f <depth file>
Required:
-db <database name>
: Database name for TASUKE
-u <user>
: User name
-p <password>
: Password for the database
-c <condition_id>
: Condition ID(name)
Optional:
-h <remote host>
: To connect remote host name
-r : Delete the conditon and tables from database.
The annotation track on the TASUKE browser can be added from GFF files.
$ tasuke_track_gff.pl -db <database name>
-u <user>
-p <password>
-f <annotation file>
-t <track name>
Required:
-db <database name>
: Database name for TASUKE
-u <user>
: User name
-p <password>
: Password for the database
-f <annotation file>
: GFF(3) formatted file
-t <track name>
: It sets here is directoly used for track name on TASUKE
Optional:
-h <remote host>
: To connect remote host name
-r : Delete the annotations from database.
$ tasuke_track_gff.pl -r -db <database name>
-u <user>
-p <password>
-t <track name>
The phenotype data can be added for using GWAS function on TASUKE.
$ tasuke_phenotype.pl -db <database name>
-u <user>
Required:
-db <database name>
: Database name for TASUKE
-u <user>
: User name
Optional:
-h <remote host>
: To connect remote host name
-r : Delete the phenotype data from database.
<password>
> Where is phenotype data csv file?
(File format: Breed Name,Phenotype,Phenotype Value)
#
<phenotype data file(.csv)>
> Where is qqman output file?
#
<qqman output file(.txt or .tsv)>
> What is a phenotype of the file?
#
<phenotype>
> Completed.
> Read the next file? [y/N]
#
y: > Where is qqman output file?
# N: Done.
$phenotypeFlg = "true";
To use the System phylogenetic tree, first create a distance matrix and set its path in config file.
There are two ways to create a distance matrix:
- 1. Use tasuke_tree_dmatrix.pl
-
Use script included in this package to create a distance matrix from TASUKE database contents.
This script calculates distances by comparing the presence or absence of variants between accessions.Command:
$ tasuke_tree_dmatrix.pl -db
<database name>
-u<user>
-p<password>
-o<outfile>
Required:
-db<database name>
: Database name for TASUKE
-u<user>
: User name
-p<password>
: Password for the database
-o<outfile>
: Distance matrix path
Optional:
-h<remote host>
: To connect remote host name
-r<order file>
: Target accession list file(Generally tasuke_www/conf/order.conf) (Default: all Accessions)
-c<target chrs>
: Target chromosomes separated by commas(Default: all Chromosomes)
-m<calc method>
: Distance matrix calculation method. simple(default)/jaccard/dice/soergel
-a : Check DEPTH=NULL and if so, set "NA" to that position. Depth information must be registered. It takes a lot of time
-b : [Use with "-a"] Store DEPTH=NULL positions on memory. Can be faster but uses more memory
-n : [Use with "-a"] Crosses all accessions and skips aggregation for position columns with DEPTH=NULL.
-l : Leave binary table file with name "<outfile>
.btbl". This file can be reused for distance calculation by converter/makeBinaryDistanceMatrix
Running this script usually takes tens of minutes. You can create a more accurate distance matrix by specifying "-a" option, but it can take hours to days. Specifying "-b" option with "-a" makes the calculation several times faster, but requires more memory.
It takes a lot of time to create binary table, which is a product on the way, but it takes only a short time to create a distance matrix from it. You can specify "-l" option to leave the binary table file unerased and resume from the distance matrix creation step. - 2. Prepare a distance matrix in your own way
- You can use a distance matrix created by an external analysis tools(R, etc.). Distance matrix format must be square matrix or lower-triangular. AccessionID must be used as sample name and must include all Accessions used by TASUKE.
In the next step, set distance matrix path to a 'tasuke_www/conf/config.php'. <outfile>
must be placed in a location that the www user has permission to read.
<outfile>
";
If you left the binary table file with "-l" option, you can recreate distance matrix with the command below. You can respecify "-m" and "-n" options. Distance matrix is output to STDOUT.
$ converter/makeBinaryDistanceMatrix -i <outfile.btbl>
[optional] > <outfile2>
Required:
-i <outfile.btbl>
: Binary table file(0/1 CSV table)
Optional:
-m <calc method>
: Distance matrix calculation method. simple(default)/jaccard/dice/soergel
-n : Crosses all accessions and skips aggregation for position columns with DEPTH=NULL.
This tool supports installation of TASUKE. It automatically detects any datasets and load the data to a database. It treats each file name as registered ID. Before running the tool, confirm relation of file names and accession ID.
Unified installer does not support GWAS and system phylogenetic tree registration.
$ install.sh <TASK>
<Option>
TASK (Required):
all : All installation processes
init : Setting defalut tables to a database
acc : Accession informtaion
ref : Reference sequence
ann : Annotation
var : Variants
tsv : Read depth or General purpose track (defalut: read depth)
Option:
-h : Help
-r : Delete specified datasets from the database.
-g : TSV file load to general purpose track.
Set your server environment to a 'install.conf' to run the 'install.sh'. And place the install.conf in same directory as install.sh.
Modifying install.conf
##### Configuration #####
#Path of 'tasuke_bin'
SCRIPTS='/PATH/tasuke_bin/'
#Database
#mysql or oracle
BACKEND='mysql
or oracle
'
#Database connection
DB=<database name>
USER=<user>
PASS=<password>
#For oracle
TABLESP=<tablespace name>
#Directory for datasets
# 'install.sh' searches for datasets in following directories. And it set the datasets to the database.
# For example, this tool searches for VCF file in './tasuke_sample_data/variants/', when setting variants to the database.
#Datasets
DATADIR='/PATH/tasuke_sample_data/'
#Enter the fasta file name you use as reference genome. not a directory.
DIR_FASTA='./reference.fasta'
#This scripts searches for '.gff' from in 'DIR_GFF'.
DIR_GFF='./'
#This scripts searches for '.vcf' from in 'DIR_VCF'.
DIR_VCF='./variants/'
#This scripts searches for '.tsv' from in 'DIR_TSV'.
DIR_TSV='./depth/'
#File format of your VCF files ['samtools' or 'gatk']
VCF='gatk'
#########################
In above case, the tool searches for any file from /PATH/tasuke_sample_data/ and load the file to the database.
e.g.) The tool searches for any files from '/PATH/tasuke_sample_data/variants/'. If the tool finds 'human001.vcf', it load the vcf to the table for human001 in your database.
Starting TASUKE
First, set below configuration at least.
Modifying conf/config.php$db = <database name>
;
$host = 'localhost' or <hostname>
;
$user = <user name>
;
$pswd = <password>
;
Access the server by web browser.
if you allocated tasuke_www/* to /(Documentroot)/tasuke/, access the following URL.
http://your_domain/tasuke
A web browser which can accept HTML5 is required. We checked the operation of TASUKE with Internet Explore(9 or later), Firefox and Google Chrome on Win and Mac.
If the TASUKE does not work, see this document.
Additional setting (Optional)
Security setting for exposing on the internet.
1. Limited-mysql-user for security protection$ mysql -u <user>
-p
> Enter password: <password>
$ mysql> create user '<new user>
'@'<hostname>
';
$ mysql> set password '<new user>
'@'<hostname>
'=password('<new password>
');
$ mysql> grant select on <database name>
.* to '<new user>
'@'<hostname>
';
$ mysql> flush privileges;
$ mysql> exit;
$user = <new user>
;
$pswd = <new password>
;
Modifying /etc/httpd/conf/httpd.conf
<Apache document root>
/conf" >Order deny,allow
Deny from all
</Directory>
Using database compression, data size will be reduce and the performance is slightly improve. Particularly TSV (depth and general-purpose) data size will be reduce to 1/2 to 1/6.
The TASUKE (database) does not work until finishing this processes.
Compressed database can not be update (read-only).
If you want to update data after making compressed database, decompressing is needed.$ service mysqld stop
Move to the database directory$ cd <mysql database directory>
(default: /var/lib/mysql/<database name>
)
<tsv table>
indicates dx_accession or dx_accession_cstmMyisampack and myisamchk are repeated for each accession
$ myisampack -v <tsv table>
$ myisamchk -rq --sort-index --analyze <tsv table>
.MYI
$ service mysqld start
Load the tables$ mysql -u <user>
-p
> Enter password: <password>
$ mysql> flush tables;
$ mysql> exit;
$ service mysqld stop
Deompressing the tables$ myisamchk --unpack <tsv table>
$ service mysqld start
Load the tables$ mysql -u <user>
-p
> Enter password: <password>
$ mysql> flush tables;
$ mysql> exit;
How to update
This section describes how to update a TASUKE.
1. Unpack & CopyAfter download TASUKE package, set "tasuke_www" to the Apache document root.
Run the below commands, your configuration files (conf/config.php and order.conf) are overwrited. We recommend conducting a backup of your configuration file before update.
$ tar xf ./tasuke_tools.tar
$ cp -r ./tasuke_tools/tasuke_www/* <TASUKE DIRECTORY>
$ tasuke_db_upgrade.pl -db <database name>
-u <user>
-p <password>
Required:
-db <database name>
: Database name for TASUKE
-u <user>
: User name
-p <password>
: Password for the database
Set any items to the updated configuration file.
More detail: Configuration-page