A stand-alone application for constructing websites for visualizing and browsing synteny blocks
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
- 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
git clone https://github.com/jkimlab/mySyntenyPortal.git
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 buildTo 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]
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 [email protected] -
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 [email protected] -
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]
- 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/)