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/)

Contact

bioinfolabkr@gmail.com

RyanBalfanz/mySyntenyPortal