CRISPR-X Server and Database Manual
1.Dependence
| Name | Version | Notes |
| Linux | Fedora release 10 (Cambridge) | |
| PHP | 5.2.9 | |
| Python | 2.5.2 or higher 2.X version | |
| MySQL | 5.0.88 | |
| MySQL Connector | 6.1 | Connector/C (libmysqlclient).
It will be downloaded on installation automatically. |
| RNAfold | 2.1.8 | This software is free, and should be installed globally. |
| ImageMagick | 6.4.0 | This software is free, and should be installed globally. And CLI supports. |
2.Deployment
For database, CasDB, please fellow this instruction step by step:
1.On your server, unpack the source code, redirect into the folder 'CasDB' under 'server' directory. Please pay attention that the compressed file 'CasDB.tar.gz' is for our automatic test on Travis CI. It’s useless for CasDB deployment!
2.Make a new folder named 'database' under 'CasDB'. Next, download model organism genome data into this folder. We use data from NCBI database. Temporally support these fellow model organisms
| Model Organism | Data Source |
| E.coli-k12-MG1655 | ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/ |
| Saccharomyces_cerevisiae | ftp://ftp.ncbi.nih.gov/genomes/Fungi/Saccharomyces_cerevisiae_uid128/ |
| Arabidopsis_thaliana | ftp://ftp.ncbi.nih.gov/genomes/Arabidopsis_thaliana/ |
| Drosophila_melanogaster | ftp://ftp.ncbi.nih.gov/genomes/Drosophila_melanogaster/ |
The whole directory structure should look like this:
-server
-CasDB
-getGeneInfo.py
- sgRNAimport.py
-database
-[Species Name]
-[Chromosome Name]
-[Data files, we need ffn, fna, ptt files]
3.Then create a new database, rename it as you like. Using this database, execute 'CasDB.sql' and then execute 'view.sql'.
4.Configure the python script, 'getGeneInfo.py'. Just modify one line according your environment and setup:
db = MySQLdb.connect("YOUR-DB-HOST","DB-USERNAME","DB-PASSWD","DB-NAME" )
Then run this python script by typing 'python getGeneInfo.py' in command line interface. This script will work automatically to recognize the species name and chromosomes. Besides this, more gene information will be calculated and inserted into CasDB. But it may take some time.
5.Configure the python script, 'sgRNAimport.py'. Just as above modify one line according your environment and setup:
db = MySQLdb.connect("YOUR-DB-HOST","DB-USERNAME","DB-PASSWD","DB-NAME" )
Then run this python script by typing 'python sgRNAimport.py' in command line interface. This script will work automatically to recognize the species name and chromosomes. Besides this, sgRNA will be found and inserted into CasDB. But it may take some time.
For server, we provide an install shell script to operate a one-click install. You just run the 'install.sh' and it will help you install the whole system. The last step for server deployment is to configure PHP scripts. It’s very easy. Just modify 'server/config.php' according to guides in the source file.
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