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Virtual Pharmacist is a web tool that interprets personal genome for the impact of genetic variation on drug response. It can take variants data (VCF format), microarray SNP genotyping data and high-throughput sequencing data as input, and report to the users how the variants in their personal genomes impact their drug response, including drug e…
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The configuration of Virtual Pharmacist Virtual Pharmacist is a free and open source web-based platform for personal genome interpretation. Please follow steps below to setup the platform successfully in your own server. 1: Be sure to start the web service of your own server, such as apache and nginx 2: Put all of the contents of the folder to the default folder for the website. for apache, the default folder storing the website is /var/www/html/ 3: specify the parameters of web service so as to support the file uploading from browser. file_uploads=On; //allow the file uploading from the web browser upload_max_filesize=20M //set the maximum size of the uploading file post_max_size=80M //set the maximum size for posting the file to web server 4: Database configuration At UNIX shell, type: mysql -uroot -p[your_root_password] After connecting to MySQL, type: create database vp; create user vp@localhost identified by 'vp123456'; grant all privileges on vp.* to vp; disconnect and then import the vp.sql database file into vp database by typing: mysql -u vp -p vp < vp.sql; The PHP script to communicte with the mysql database just created is mysql_connect.php 5: make sure that you have enabled port 22 for uploading high-throughput sequence data by FTP 6: Configuration of the uploading interface: 1): open upload_js.php,upload1_js.php,upload2_js.php,upload3_js.php 2) change the url of sustc-genome.org.cn to your own url in the following files a): upload_js.php flash_url : ""http://sustc-genome.org.cn/vp/upload_file/swfupload/swfupload.swf upload_url: ""http://sustc-genome.org.cn/vp/upload_file/upload.php b): upload1_js.php flash_url : ""http://sustc-genome.org.cn/vp/upload_file/swfupload/swfupload.swf upload_url: ""http://sustc-genome.org.cn/vp/upload_file/upload1.php c): upload2_js.php flash_url : ""http://sustc-genome.org.cn/vp/upload_file/swfupload/swfupload.swf upload_url: ""http://sustc-genome.org.cn/vp/upload_file/upload2.php d): upload3_js.php flash_url : ""http://sustc-genome.org.cn/vp/upload_file/swfupload/swfupload.swf upload_url: ""http://sustc-genome.org.cn/vp/upload_file/upload3.php 3): Uploaded file destinations a): microarray data: ./upload_file/tmp_data b): VCF data: ./upload_file/vcf_data c): multiple sample VCF data ./project 7: Configuration of high-throughput sequence analysis pipeline 1): index building for human genome. a): download the hg19.fa from the UCSC ftp and put it into ./bin/hg19 b): change directory to the ./bin/hg19 c): index the hg19.fa by bowtie2: bowtie2-build hg19.fa hg19 (make sure that six index .bt files will be generated by bowtie2 after the indexing process) 8: Remarks Check whether all folders and files are granted the appropriate privileges. Please contact your system administrator for help if needed.
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Virtual Pharmacist is a web tool that interprets personal genome for the impact of genetic variation on drug response. It can take variants data (VCF format), microarray SNP genotyping data and high-throughput sequencing data as input, and report to the users how the variants in their personal genomes impact their drug response, including drug e…
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