mySyntenyPortal

A stand-alone application for constructing websites for visualizing and browsing synteny blocks

Quick start

git clone https://github.com/jkimlab/mySyntenyPortal.git
cd mySyntenyPortal
perl ./install.pl build
sudo perl ./install.pl install
perl ./mySyntenyPortal build -conf ./configurations/sample.conf

System requirements

Linux x64
Apache >= 2.2.15
zlib >= 1.2.8
ImageMagick >= 6.7.x
Perl >= 5.8.x or new
Perl modules

To list all required perl modules, use the command below.

perl ./src/check_modules.pl

Download source

git clone https://github.com/jkimlab/mySyntenyPortal.git

Installing mySyntenyPortal

To install mySyntenyPortal, use the 'install.pl' perl script.

Usage:  ./install.pl [build|install|clean] <parameters>

 ** It requires a 'sudo' privilege for the 'install' command. **

Simple examples:
    ./install.pl build
    ./install.pl install
    ./install.pl clean

Commands:
    build    =>  complile third party tools and set path information
    install  =>  make a symbolic link in the web root directory
    clean    =>  clean up third party tools and remove the symbolic link in the web root directory

Parameters:
  [ install ]
    -webroot_path|w => Apache web root path (default: /var/www/html)
    -manager_name|m => Website manager name (default: mySyntenyPortal)

  [ clean ]
    -manager_name|m => Website manager name (default: mySyntenyPortal)

Examples

You can compile mySyntenyPortal and set your own path information by one command below.
```
./install.pl build
```
To access web interfaces, mySyntenyPortal makes a symbolic link in the web root directory.
```
sudo ./install.pl install
sudo ./install.pl install -webroot_path [Webroot directory path]
sudo ./install.pl install -manager_name [Website manager name]
```
To clean up mySyntenyPortal, use a command below.
```
sudo ./install.pl clean -manager_name [Website manager name]
```

When mySyntenyPortal is successfully installed, you can access the website manager

Default
```
http://your.host/mySyntenyPortal
```
In case of setting the custom website manager name
```
http://your.host/[Website manager name]
```

Building or removing a website

To build or remove a website, you need to write a configuration file. Then, you can use the 'mySyntenyPortal' perl script.

Usage:  ./mySyntenyPortal [build|remove] <parameters>

  ** It may require a 'sudo' privilege. **

Simple examples:
    ./mySyntenyPortal build -p 10 -conf ./configurations/sample.conf
    ./mySyntenyPortal remove -website_name Sample_website

Commands:
    build              => build a website
    remove             => remove a website

Parameters:
  [ build ]
    -conf|c            => Configuration file
    -core|p            => Number of threads (default: 10)

  [ remove ]
    -website_name|w    => Website name
    -conf|c            => Configuration file

Examples

To build a website

./mySyntenyPortal build -conf [configuration file]

To remove a website

./mySyntenyPortal remove -website_name [Website name]

Configuration file

You can build a website by using two types of input data which are assembly sequences or synteny block definitions.

With assembly sequences

    # Website name (REQUIRED)
    >Website_name
    Example

    # Input Assemblies (REQUIRED)
    # FASTA format (https://en.wikipedia.org/wiki/FASTA_format)
    >Assemblies
    Human   ../data/example_inputs/human.fa
    Mouse   ../data/example_inputs/mouse.fa
    Cow ../data/example_input/cow.fa

    # Divergence times (REQUIRED)
    # Example) Human-chimpanzee: near, Human-mouse: medium, Human-chicken: far
    >Divtimes
    Human,Mouse medium
    Human,Cow   medium
    Mouse,Cow   medium

    # Resolutions (REQUIRED)
    # The minimum size of synteny blocks in base pair
    >Resolutions
    150000,300000,400000,500000

    # Gene annotations of references (OPTIONAL)
    # Gene transfer format (GTF) (https://en.wikipedia.org/wiki/Gene_transfer_format)
    >Annotation
    Human   ../data/example_inputs/Homo_sapiens.GRCh38.87.gtf.gz
    Mouse   ../data/example_inputs/Mus_musculus.GRCm38.87.gtf.gz

    # Cytogenetic bands (OPTIONAL)
    # Column 1: Chromosome
    # Column 2: Start position
    # Column 3: End position
    # Column 4: Name of cytogenetic band
    # Column 5: Giemsa stain results
    # Refer to the sample files '[mySyntenyPortal_root]/data/example_input/Human.cytoband'
    >Cytoband
    Human   ../data/example_inputs/Human.cytoband
    Mouse   ../data/example_inputs/Mouse.cytoband
    Cow ../data/example_inputs/Cow.cytoband

    # Pre-built circos plots (OPTIONAL)
    # If you want to visualize all chromosomes/scaffolds, you can write 'all' instead of specific chromosomes
    >circos1
    resolution:150000
    Human:chr1,chr3,chr5,chr6,chr8,chr12,chr15,chr19
    Mouse:chr1,chr3,chr7,chr17,chr18
    Cow:chr3,chr9,chr10,chr14,chr17,chr22

    # Email address is used to make a contact link in published website. (OPTIONAL)
    >Email
    Your@e-mail.com

With synteny block definitions

    # Website name (REQUIRED)
    >Website_name
    Example

    # Input synteny blocks (REQUIRED)
    # 
    # Example)
    # 
    # >1
    # Human.chr1:933237-58547094 +
    # Mouse.chr4:103313481-156255944 -
    #
    # >2
    # Human.chr1:58654678-67136459 +
    # Mouse.chr4:94941999-103299247 +
    #
    # Refer to the sample file '[mySyntenyPortal_root]/data/example_input/human.mouse.synteny'
    >Synteny_blocks
    Human,Mouse ../data/example_inputs/human.mouse.synteny
    Human,Cow   ../data/example_inputs/human.cow.synteny

    # Genome size files (REQUIRED)
    #
    # Column1: Chromosome/scaffold_name
    # Column2: Length
    # 
    # Example
    # chr1  249250621
    # chr2  243199373
    # 
    # How to make?
    # [mySyntenyPortal_root]/src/third_party/kent/faSize -detailed [FASTA] > [size file]
    >Genome_size
    Human   ../data/example_inputs/human.sizes
    Mouse   ../data/example_inputs/mouse.sizes
    Cow ../data/example_inputs/cow.sizes

    # Gene annotations of references (OPTIONAL)
    # Gene transfer format (GTF) (https://en.wikipedia.org/wiki/Gene_transfer_format)
    >Annotation
    Human   ../data/example_inputs/Homo_sapiens.GRCh38.87.gtf.gz
    Mouse   ../data/example_inputs/Mus_musculus.GRCm38.87.gtf.gz

    # Cytogenetic bands (OPTIONAL)
    # Column 1: Chromosome
    # Column 2: Start position
    # Column 3: End position
    # Column 4: Name of cytogenetic band
    # Column 5: Giemsa stain results
    # Refer to the sample files '[mySyntenyPortal_root]/data/example_input/Human.cytoband'
    >Cytoband
    Human   ../data/example_inputs/human.cytoband
    Mouse   ../data/example_inputs/mouse.cytoband
    Cow ../data/example_inputs/cow.cytoband

    # Pre-built circos plots (OPTIONAL)
    # If you want to visualize all chromosomes/scaffolds, you can write 'all' instead of specific chromosomes
    >circos1
    Human:chr1,chr3,chr5,chr6,chr8,chr12,chr15,chr19
    Mouse:chr1,chr3,chr7,chr17,chr18
    Cow:chr3,chr9,chr10,chr14,chr17,chr22

    # Email address is used to make a contact link in published website (OPTIONAL)
    >Email
    Your@e-mail.com

Converting synteny block definitions

With synteny block built by Cinteny

    ./scripts/convert_synteny/Cinteny2CS.pl [Input synteny block] [Output synteny block]

With synteny block built by Satsuma

    ./scripts/convert_synteny/Satsuma2CS.pl [Input synteny block] [Output synteny block]

With synteny block built by SyntenyTracker

    ./scripts/convert_synteny/SyntenyTracker2CS.pl [Input synteny block] [Output synteny block]

Third party tools

Bedtools (http://bedtools.readthedocs.io/en/latest/)
KentUtils (http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads)
LASTZ (http://www.bx.psu.edu/~rsharris/lastz/)
inferCars (http://www.bx.psu.edu/miller_lab/car/)
Circos (http://circos.ca/)

How to cite

Lee J, Lee D, Sim M, Kwon D, Kim J, Ko Y, Kim J. mySyntenyPortal: an application package to construct websites for synteny block analysis. BMC Bioinformatics. 2018 Jun 5;19(1):216. doi: 10.1186/s12859-018-2219-x.

Contact

bioinfolabkr@gmail.com

jkimlab / mySyntenyPortal

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