Team:UESTC-Software/Installation.html

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<h2>Step4: Enjoy it!</h2>
<h2>Step4: Enjoy it!</h2>
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<h1>CRISPR-X Server and Database Manual</h1>
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<h2>1.Dependence</h2>
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<table border="1px" cellspacing="0px" style="border-collapse:collapse;word-break:break-word;border-color: #c7d3af;
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color: #999;font-size: 15px;">
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<tr><td>Name</td><td>Version</td><td>Notes</td></tr>
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<tr><td>Linux</td><td>Fedora, Ubuntu, Debian or related system</td><td>Here, related system means that the Linux distribution supports <span style="color:#8fc41f">'.rpm'</span> or <span style="color:#8fc41f">'.deb'</span> packages. </td></tr>
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<tr><td>PHP</td><td>5.2.9 or higher version</td><td></td></tr>
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<tr><td>Python</td><td>2.5.2 or higher 2.X version</td><td></td></tr>
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<tr><td>MySQL</td><td>5.0.88</td><td></td></tr>
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<tr><td>MySQL Connector</td><td>6.1</td><td>Connector/C (libmysqlclient).
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It will be downloaded on installation automatically. </td></tr>
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<tr><td>RNAfold</td><td>2.1.8</td><td>This software is free, and should be installed globally. </td></tr>
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<tr><td>ImageMagick</td><td>6.4.0</td><td>This software is free, and should be installed globally. And CLI supports. </td></tr>
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</table>
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<h2>2.Deployment</h2>
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<p>Firstly, you need to execute the shell script, 'install.sh' under 'server' folder, which helps you to install dependencies automatically and compile our auxiliary programs. Then goes to database and server configure. </p>
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<p>For database, CasDB, please fellow this instruction step by step:</p>
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<p>1.On your server, unpack the source code, redirect into the folder <span style="color:#8fc41f">'CasDB'</span> under <span style="color:#8fc41f">'server'</span> directory. Please pay attention that the compressed file <span style="color:#8fc41f">'CasDB.tar.gz'</span> is for our automatic test on Travis CI. It’s useless for CasDB deployment! </p>
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<p>2.Make a new folder named <span style="color:#8fc41f">'database'</span> under <span style="color:#8fc41f">'CasDB'</span>. Next, download model organism genome data into this folder. We use data from NCBI database. Temporally support these fellow model organisms</p>
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<table border="1px" cellspacing="0px" style="border-collapse:collapse;word-break:break-word;border-color: #c7d3af;
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color: #999;">
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<tr><td>Model Organism</td><td>Data Source</td></tr>
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<tr><td>E.coli-k12-MG1655</td><td>ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/</td></tr>
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<tr><td>Saccharomyces_cerevisiae</td><td>ftp://ftp.ncbi.nih.gov/genomes/Fungi/Saccharomyces_cerevisiae_uid128/</td></tr>
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<tr><td>Arabidopsis_thaliana</td><td>ftp://ftp.ncbi.nih.gov/genomes/Arabidopsis_thaliana/</td></tr>
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<tr><td>Drosophila_melanogaster</td><td>ftp://ftp.ncbi.nih.gov/genomes/Drosophila_melanogaster/</td></tr>
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</table>
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<p>The whole directory structure should look like this:</p>
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<pre style="font-size: 14px;color: #8fc41f;line-height: 1.5em;max-width: 44em">
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-server
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    -CasDB
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        -getGeneInfo.py
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        - sgRNAimport.py
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        -database
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            -[Species Name]
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                -[Chromosome Name]
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                    -[Data files, we need ffn, fna, ptt files]
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</pre>
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<p>3.Then create a new database, rename it as you like. Using this database, execute <span style="color:#8fc41f">'CasDB.sql'</span> and then execute <span style="color:#8fc41f">'view.sql'</span>. </p>
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<p>4.Configure the python script, <span style="color:#8fc41f">'getGeneInfo.py'</span>. Just modify one line according your environment and setup:
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<br/><b>db = MySQLdb.connect("YOUR-DB-HOST","DB-USERNAME","DB-PASSWD","DB-NAME" )</b></p>
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<p>Then run this python script by typing <span style="color:#8fc41f">'python getGeneInfo.py'</span> 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.</p>
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<p>5.Configure the python script, <span style="color:#8fc41f">'sgRNAimport.py'</span>. Just as above modify one line according your environment and setup:<br/><b>db = MySQLdb.connect("YOUR-DB-HOST","DB-USERNAME","DB-PASSWD","DB-NAME" )</b></p>
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<p>Then run this python script by typing <span style="color:#8fc41f">'python sgRNAimport.py'</span> 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.</p>
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<p>For server, you must configure PHP scripts manually. It’s very easy. Just modify <span style="color:#8fc41f">'server/config.php'</span> according to guides in the source file. </p>
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Latest revision as of 19:10, 17 October 2014

UESTC-Software

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