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

README.md

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

Contact

bioinfolabkr@gmail.com

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