TASUKE - Configuration

Configuration

TASUKE : Configuration file (config.php)

Edit a configuration file as below. The location of the file is "(Apache DocumentRoot)/conf/config.php".

MySQL Database section

Set about database connection to this section.

Modifying conf/config.php

Set the name of MySQL database

$db = "<database name>";

Set the host name

$host = "localhost or hostname";

Set the user name of MySQL

$user = "<user name>";

Set the password of MySQL

$pswd = "<password>;"

Back-end database

Set about kind of database to this section. Currently, only MySQL is supported.

Modifying conf/config.php

Back-end database
mysql: It requires php-mysql module.
$backend="mysql";

Temporary directory

A directory where temporary files such as phylogenetic tree creation are stored. If it does not exist, TASUKE will try mkdir.

Modifying conf/config.php

Temporary directory(for Phylogenetic tree)
$tempdir="/tmp/tasuke_tmp";

Serial table auto detection

When registering a large number(> 900) of Chr/Contig reference seqs, table is divided(SerialTable). If you want to use SerialTable, you have to turn ON(1) its auto-detection.
Normally, set it to OFF(0) to reduce server load.
If you are using SerialTable and this value is OFF(0), you will get a warning on web browser.

Modifying conf/config.php

Whether to automatically determine if the table is divided or not?
$autoDetectSerialTable = 0 or 1;

Redis connection (Beta)

Set about Redis connection to this section.

Modifying conf/config.php

Cache system using Redis (Beta)
Set "enabled" or "disabled" to $useRedis.
$useRedis = "disabled or enabled";
$redisHost = "localhost or hostname";
$redisPort = "6379 or port number";
$redisDBName = "0 or database name";

Naming of reference genome

This name is used for the name of reference sequence.

Modifying conf/config.php

$reference = "Reference";

Making external link on the annotation (GFF) track

This link enable users to jump external page by clicking the structure of the annotation.

e.g.)
1. Set "http://tasuke.com/search?=" to the $external_link and click "transcript001" on the track, the link destination URL will be set to "http://tasuke.com/search?=transcript001".
2. Set ".html" to the $external_link_suffix and click "transcript001" on the track, link destination URL will be set to "http://tasuke.com/transcript001.html".

Modifying conf/config.php

External link URL on the annotation track

$external_link = "<Destination URL>";

Suffix for external URL link

$external_link_suffix = "<suffix for the URL>";

This value means a tag from gff file for external link url parameter.
If you set undefined tag to this value, it automatically sets "ID" to this value.

$external_link_tag_gff = "<tag name>";

If you have multiple Tracks and want to set different links for each, set as follows:

Modifying conf/config.php

External links for each tracks
The value set here has priority over $external_link/$external_link_tag_gff/$external_link_suffix.
$external_sites = array(
  '<Track name1>' => array(
    'link' => "<Destination URL1>",
    'tag_gff' => "<tag name>",
    'suffix' => "<suffix for the URL>"
  ),
  '<Track name2>' => array(
    'link' => "<Destination URL2>",
    'tag_gff' => "<tag name>",
    'suffix' => "<suffix for the URL>"
  )
);

Making head of chromosome name

If the chromosome name of the reference fasta is only numbers or alphabets, you can add a word like "chr" by setting here.

e.g.)
"1" to "chr1"

Modifying conf/config.php

$chromosome_name = "";

Setting GWAS flag

If you show GWAS plot, you set phenotype flag true.
If you hide GWAS plot, you set phenotype flag false.

Modifying conf/config.php

$phenotypeFlg = "true";

Setting System phylogenetic tree

If you use system phylogenetic tree function, create a distance matrix file in advance. You can use the system phylogenetic tree by specifying that path in $distanceMatrixPath.

Modifying conf/config.php

[SystemTree] use system tree function.
// Specify a distance matrix file in Phylip format(Lower-triangle matrices).
// https://evolution.gs.washington.edu/phylip/doc/distance.html
// if $distanceMatrixPath is empty or not found, tree function will not be used.
$distanceMatrixPath = "";

// Do you want to display tree by default at startup?
$systreeDefaultOn = 1;

// [System/PhylipTree] Branches whose height is greater than this value will collapsed.
// Float. Invalid if 0 or empty.
$systreeAutoCollapseThreshold = 0;

// What to consider for $systreeAutoCollapseThreshold. (height/ratio)
$systreeAutoCollapseType = "height";

// [System/PhylipTree] Other options
// - Correction: ""/asec/pow/cdf
$systreeCorrection = "";

// - SortType: height or subtree
// height : max height of subtree
// subtree: number of subtree leaves
$systreeSortType = "subtree";

// - SortType: "" or asc or desc
$systreeSort = "desc";

// - TreeWidth: int
$systreeWidth = "100";

Setting the number of threads

Set more threads , get fasta sequence and phylogenetic tree faster.

Modifying conf/config.php

$threadnum = "4";

Setting gene id column number

To get gene ID information on ANN/EFF information , set column number.
If you can't get correct information on SNP detail information , change correct number.

Modifying conf/config.php

$ANNcol = "6";

$EFFcol = "7"; //for older snpEff annotation

$EFFcol = "8";

For primer designing

Primer designing function requires Primer3 and MFEprimer(optional). Set path of Primer3 and MFEprimer to this section. (Primer3 version 2.3.0 or later, MFEprimer version 2.0 or later(MFEprimer3 is not supported))

Modifying conf/config.php

Primer3

$primer3Path = "<path/primer3_core>";

Primer3 thermodynamic parameters

$primer3ThermPath = "<path/primer3_config>";

MFEprimer path

$MFEpath = "<path/MFEprimer.py>";

MFEprimer reference genome database path

$MFEDBpath = "<path/reference/reference.fasta>";

If the primer3 does not work on the TASUKE, try the following commands.

Install SELinux policy management tool

$ yum install policycoreutils-python

Change SELinux security context

$ semanage fcontext -a -s system_u -t httpd_sys_content_t "<PRIMER3_DIRECTORY>";

$ restorecon -RF "<PRIMER3_DIRECTORY>";

For phylogenetic analysis

Phylogenetic analysis requires PHYLIP. Set path of PHYLIP to this section.

Modifying conf/config.php

$phylipDir = "/PATH/";

If the PHYLIP does not work on the TASUKE, try same commands as primer3 section.

For BLAST search

BLAST search requires ncbi blast+ tools. Set path of BLAST to this section.
$blastDBPath must be a DB file created by makeblastdb with "-parse_seqids" option.

Modifying conf/config.php

BLAST PATH

$blastPath = "path/bin/blastn";

BLAST reference genome database PATH

$blastDBPath = "path/reference/reference.fasta";

Maximum level of zoom for viewing each nucleotide

Limit of displaying each snps and indels when absolute position mode.

Modifying conf/config.php

$nuc_max = "100k";

General purpose track (Custom track)

Visualizing BAM, BED and BEDGrpah. (RNA-seq read depth, CHIP-seq, BS-seq...)
If you want to use this feature, Set "enabled" to the $customTrack.

Modifying conf/config.php

Set "enabled" or "disabled" to $customTrack.

$customTrack = 'enabled' or 'disabled';

For more detail setting, see following items.

Modifying conf/config.php

Track name for menu

$customTrackName = <track name>;

Kind of data name (Unit)

$customTrackKindofData = <unit>;

Normalizing based on number of read or not
It normalizes a value using header value of TSV file. It is useful for RNA-seq data.
Set "enabled" or "disabled" to $customTrackNormByRead.

$customTrackNormByRead = 'enabled' or 'disabled';

Change color gradiation for custom track

$cstm_max = 1000;

$cstm_min = 0;

Accession name

Canvas width for accession ids and groups

Modifying conf/config.php

$accession_cvs_width = 160;

Set any color to each accession groups(variety, sub varienty, origin, type).

Modifying conf/config.php

Set "enabled" or "disabled" to $color_acc_group.

$color_acc_group = 'enabled' or 'disabled';

Color definition

You can set default color for each data. And users can change each color by the color manager.

Set a hex formatted value.
e.g.) $snp_max_col="#00FF00";

Modifying conf/config.php

Color for maximum of SNP count

$snp_max_col="#00FFFF";

Color for minimum of SNP count

$snp_min_col="#F0F8FF";

Color for maximum of INDEL count

$indel_max_col="#A52A2A";

Color for minimum of INDEL count

$indel_min_col="#FFCB8E";

Color for maximum of DEPTH value

$depth_max_col="#000000";

Color for minimum of DEPTH value

$depth_min_col="#F2F2F2";

Color for maximum of custom track value

$cstm_max_col="#A229B8";

Color for minimum of custom track value

$cstm_min_col="#F5E9F7";

Color for maximum and minimum of custom track value when multiple conditions were enabled.

$cstm_max_col_para1="#77ab42";
$cstm_min_col_para1="#f1f6ec";
$cstm_max_col_para2="#a13b4b";
$cstm_min_col_para2="#f5ebed";
$cstm_max_col_para3="#1a5dd9";
$cstm_min_col_para3="#e8eefb";

Set maximum of depth value for display

This parameter designate the value for the depth color. This value is used to make a gradation corresponding to each depth value.

Modifying conf/config.php

$depth_max = 140;

$depth_min = 0;

Set count of SNP in your expectation by each zoom level

This parameter designate the value for the depth color. This value is used to make a gradation corresponding to each depth value.

Modifying conf/config.php

$snp_100k=1000;
$snp_90k=900;
$snp_80k=800;
$snp_70k=700;
$snp_60k=600;
$snp_50k=500;
$snp_40k=400;
$snp_30k=300;
$snp_20k=200;
$snp_10k=100;
$snp_9k=90;
$snp_8k=80;
$snp_7k=70;
$snp_6k=60;
$snp_5k=50;
$snp_4k=40;
$snp_3k=30;
$snp_2k=20;
$snp_1k=10;
$snp_900b=9;
$snp_800b=8;
$snp_700b=7;
$snp_600b=6;
$snp_500b=5;
$snp_400b=4;
$snp_300b=3;
$snp_200b=2;
$snp_100b=1;
$snp_90b=1;
$snp_80b=1;
$snp_70b=1;
$snp_60b=1;
$snp_50b=1;
$snp_40b=1;
$snp_30b=1;
$snp_20b=1;
$snp_10b=1;
$snp_9b=1;
$snp_8b=1;
$snp_7b=1;
$snp_6b=1;
$snp_5b=1;
$snp_4b=1;
$snp_3b=1;
$snp_2b=1;
$snp_1b=1;
$snp_min=1;

Set count of INDEL in your expectation by each zoom level

This parameter designate the value for the depth color. This value is used to make a gradation corresponding to each depth value.

Modifying conf/config.php

$indel_100k=1000;
$indel_90k=900;
$indel_80k=800;
$indel_70k=700;
$indel_60k=600;
$indel_50k=500;
$indel_40k=400;
$indel_30k=300;
$indel_20k=200;
$indel_10k=100;
$indel_9k=90;
$indel_8k=80;
$indel_7k=70;
$indel_6k=60;
$indel_5k=50;
$indel_4k=40;
$indel_3k=30;
$indel_2k=20;
$indel_1k=10;
$indel_900b=9;
$indel_800b=8;
$indel_700b=7;
$indel_600b=6;
$indel_500b=5;
$indel_400b=4;
$indel_300b=3;
$indel_200b=2;
$indel_100b=1;
$indel_90b=1;
$indel_80b=1;
$indel_70b=1;
$indel_60b=1;
$indel_50b=1;
$indel_40b=1;
$indel_30b=1;
$indel_20b=1;
$indel_10b=1;
$indel_9b=1;
$indel_8b=1;
$indel_7b=1;
$indel_6b=1;
$indel_5b=1;
$indel_4b=1;
$indel_3b=1;
$indel_2b=1;
$indel_1b=1;
$indel_min=1;

TASUKE : Other settings

Page layout

header
Modifying docs/top.html

footer
Modifying docs/bottom.html

Order of the accessions / hide the accessions

In initially state, TASUKE loads the accessions that was sorted by installation order. this order is based on the accession information that is using as a input file of "tasuke_accession.pl". If you want to change the order of accessions, edit a below file. In addition, you can hide any accessions by using this function. An accession that does not contain "order.conf" will be hidden on the TASUKE.

If you want to use this function, write the IDs (accessions) to each line of this file.

accession_C
accession_B
accession_A
:

This function does not work when this file contains nothing or the file does not exist on the conf directory.

Undefined IDs were found, and the Ids will be ignored.

e.g.) When your database has 5 accessions, but you want to show 3 accessions only.
The accession information in the database

accession_1
accession_2
accession_3
accession_4
accession_5

conf/order.conf

accession_5
accession_2
accession_1

On the web browser

Move to a destination region with Query string

You set several parameters for viewing destination region to URL of the TASUKE, and TASUKE views that region. It is useful for link from other web page.

e.g.) If you want to move to the 'gene001(chr01:10000-20000)' from any position or other web page, access the below URL.
http://hostname/index.html?chr=chr01&st=10000&en=20000&id=gene001

Parameter	Description
chr	Name of the sequence
st	Start position
en	End position
id	If you set transcript id to this parameter, the transcript object will be highlighted on the annotation track. (Not required)

It occurs truncation error when calculating optimum block-size (window) for the request region, so it is slightly different between the request region and viewed region.

A way of showing the designated accessions from external web page

Set the designated accessions to a query string of the URL (similar to above section). This function can use other query string functions together.

e.g.) Set 'human001,human002,human004' to the query string and access the below URL.
http://hostname/index.html?acc=human001,human002,human004

Parameter	Description
acc	Comma-separated accessions (IDs)

Server

Exposing on the internet

1. You must use limited-mysql-user for security protection. See following steps.

$ 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;

Modifying conf/config.php

$user = <new user>;
$pswd = <new password>;

2. Access limiting for the configuration files
Modifying /etc/httpd/conf/httpd.conf

<Directory "<Apache document root>/conf" >
Order deny,allow
Deny from all
</Directory>

Compressing the database

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.

Compressing

Stop the mysql-server

$ service mysqld stop

Move to the database directory

$ cd <mysql database directory> (default: /var/lib/mysql/<database name>)

Compressing the tables
<tsv table> indicates dx_accession or dx_accession_cstm
Myisampack and myisamchk are repeated for each accession

$ myisampack -v <tsv table>

$ myisamchk -rq --sort-index --analyze <tsv table>.MYI

Start the mysql-server

$ service mysqld start

Load the tables

$ mysql -u <user> -p

> Enter password: <password>

$ mysql> flush tables;

$ mysql> exit;

Decompressing

Stop the mysql-server

$ service mysqld stop

Deompressing the tables

$ myisamchk --unpack <tsv table>

Start the mysql-server

$ service mysqld start

Load the tables

$ mysql -u <user> -p

> Enter password: <password>

$ mysql> flush tables;

$ mysql> exit;

TASUKE+ multiple genome browser for variants and GWAS

Configuration