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Forecaster – GUI User Guide 1.0

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1. 8Gb recommended by 350 Mb of empty disk space without user files Lap LINUX Ubuntu 10 04 LTS CentOS 5 7 or CentOS 6 2 32 or 64 bits architecture 6 Gb of RAM memory 8Gb recommended 500 Mb of empty disk space without user files INSTALLATION PROCEDURES The following sections provide detailed procedures to install ruby and the FORECASTER Platform In the Windows environment Ruby is provided as a folder and there is no system installation required Under the Linux environment there is two options offered a system installation of Ruby or a self contained folder Please refer to either procedure according to your preferences WINDOWS INSTALLATION Version recommended Windows 7 64 bits e Executing the Forecaster platform on Windows is extremely simple and can be done in two steps The first step is to unzip the Forecaster zip into your favorite folder in the system The second step is to run start forecaster cmd The following command window will appear and the FORECASTER server will start on port 3000 As soon as this program runs your computer acts as a server You can modify the port by editing the start forecaster cmd script and changing the value in p 3000 EA C devzone InstantRails ruby bin ruby exe nml x Starting Mongrel listening at 6 6 6 6 3666 Starting Rails with production environment Rails loaded Loading any Rails specific GemPlugins Signals ready INT gt stop no restart Mongrel 1 1 5 available a
2. the required gems are installed install v 2 1 0 rails install hpricot install rubyzip install mongrel install v 1 2 4 sqlite3 ruby RUNNING THE APPLICATION The application can be started Once the installation is complete go to the forecaster directory and start the rails server using as a user not root ruby script server e production p 3000 You can modify the port changing the value in p 3000 Once the server starts open your favorite browser and navigate to http 127 0 0 1 3000 and the login screen will appear The default user can login with login admin and password fitted The forecaster application can be reached from another computer connected to the network by using the IP address of the server ex http 168 192 0 11 3000 LINUX CENTOS 6 SYSTEM INSTALLATION Version recommended CentOS 6 2 64 bits w N a Installation on Centos requires to install from the CentOS The following list of commands allows the installation of the required version of ruby EXTRACTING THE FORECASTER APPLICATION The first step is to uncompress the forecaster tgz into the folder of your choice Once the application is ready open a terminal and type the commands required for each step as described below You need to be root to perform the installation of ruby 9 INSTALLING RUBY First as root install ruby yum install ruby ruby devel Installing the dependencies install gcc
3. MOLECULAR PECASTER En Loon pomo E o E AM n D a bs i P 1 Convert E to 3D x Prepare protein pdb to mol2 Extract representative library Create combinatorial library Search for analogues Easy integration of 3rd party programs ula VASEN iiic www molec Molecular Forecaster Inc Forecaster 1 2 Server Installation Guide 13 June 2014 CONTENTS Uno c 4 BL EE 4 Installation Procedures oc vssancgussasecradsnaacsissnsonenudevncsssouaninedunentubdeanapeiudenndgnsiiaaneandalandeshdanianeiavieanters 4 Windows IS Calla ON M 4 Linux portable Installation wscsicwrceindnnacsictnesieedsuuesndcmebecdsanndsadensubacodenndandsnuubsadanncidocrusimedenstite 5 Extracting the Forecaster applibtallOfi o is trap Riera ege cna Ni etat Frac a a vaL Ie Mao EXXCH RS R Rad vk 5 Extracting the Ruby Portable Application ccccssccccssssececeesseececssueeecssseeeceeseeeeceesenaes 5 Running the Application D 5 Linux Ubuntu System Installation 2 citerior Mask uae Si qus sau Ne FER aa 0x DAR VRAC Ra REL Meo EMR o GER esq 6 Extracting the Forecaster application csi eis etit etant no R Etat Frac th a Ranae Ma REM MERE Da IE 6 Installing RUDY T S 6 Installing RODVBEITIS Lio Gasesectet tou xt Ed endi xh EE a Oe E RSEN RUN IR UN RUE ven Fa paa dv EUM Ma DIM Ro NOE iE 6 Installing the neces
4. e IP address of the server ex http 168 192 0 11 3000 LINUX CENTOS 5 SYSTEM INSTALLATION l ne M Version recommended CentOS 5 7 64 bits W Installation on Centos requires some steps to install Ruby from sources and all the required libraries since the ruby version from the CentOS repository is 1 8 5 and we need a newer version The following list of commands allows the installation of the required version of ruby EXTRACTING THE FORECASTER APPLICATION The first step is to uncompress the forecaster tgz into the folder of your choice Once the application is ready open a terminal and type the commands required for each step as described below You need to be root to perform the installation of ruby DOWNLOADING AND INSTALLING RUBY First as root create the source folder and download the source files su mkdir sources cd sources wget http ftp ruby lang org pub ruby 1 8 ruby 1 8 7 tar gz tar xvfz ruby 1 8 7 tar gz install gcc gcc ct t install zlib devel install openssl devel install readline devel install sqlite devel Building the program and installation cd ruby 1 8 7 configure with openssl dir usr lib64 openssl make make install INSTALLING RUBYGEMS Downloading the rubygems sources cd sources wget http rubyforge org frs download php 69365 rubygems 1 3 6 tgz tar xzvf rubygems 1 3 6 tgz cd rubygems 1 3 6 ruby setup rb INSTALLING THE NECESSARY LIBRARIES Rails and
5. gcc ct t install zlib devel install openssl devel install readline devel install sqlite devel INSTALLING RUBYGEMS Installing rubygems yum install rubygems INSTALLING THE NECESSARY LIBRARIES Rails and the required gems are installed install v 2 1 0 rails install hpricot install rubyzip install mongrel install sqlite3 RUNNING THE APPLICATION The application can be started Once the installation is complete go to the forecaster directory and start the rails server using ruby script server e production p 3000 You can modify the port changing the value in p 3000 Once the server starts open your favorite browser and navigate to http 127 0 0 1 3000 and the login screen will appear The default user can login with login admin and password fitted 10 The forecaster application can be reached from another computer connected to the network by using the IP address of the server ex http 168 192 0 11 3000 11 TROUBLESHOOTING LINUX HOST 1 Ruby runs at gt 90 CPU all the time To correct this issue simply reset the date by executing the following command as root or sudo date s date
6. libruby1 8 libopenssl ruby sqlite3 libsqlite3 ruby1 8 Creating the symbolic links usr bin ruby1 8 usr bin ruby usr bin ril1 8 usr bin ri usr bin rdoc1 8 usr bin rdoc usr bin irb1 8 usr bin irb INSTALLING RUBYGEMS Prior to the installation of rubygems the sources directory is created mkdir sources cd sources Then rubygems are downloaded wget http rubyforge org frs download php 55066 rubygems 1 3 2 tgz The file is next unpacked and moved to the new directory tar xzvf rubygems 1 3 1 tgz cd rubygems 1 3 1 At this point the setup process can start sudo ruby setup rb And the symbolic link is created sudo ln s usr bin gem1 8 usr bin gem INSTALLING THE NECESSARY LIBRARIES Rails and the required gems are next installed install v 2 1 0 rails install v 0 8 1 hpricot install rubyzip install mongrel RUNNING THE APPLICATION The application can be started Once the installation is complete go to the forecaster directory and start the rails server using ruby script server e production p 3000 You can modify the port changing the value in p 3000 Once the server starts open your favorite browser and navigate to http 127 0 0 1 3000 and the login screen will appear The default user can login with login admin and password fitted The forecaster application can be reached from another computer connected to the network by using th
7. llation gui revXXXX Once you execute the setup sh script it will generate a startup script start forecaster sh that has to be copied in your FORECASTER installation RUNNING THE APPLICATION The application can be started Once the installation is complete go to the forecaster directory and start the rails server using sh start forecaster sh You can modify the port changing the value in p 3000 by editing the start forecaster sh script Once the server starts open your favorite browser and navigate to http 127 0 0 1 3000 and the login screen will appear The default user can login with login admin and password fitted The forecaster application can be reached from another computer connected to the network by using the IP address of the server ex http 168 192 0 11 3000 LINUX UBUNTU SYSTEM INSTALLATION o Version recommended Ubuntu 64 bits 10 04 LTS 15 Installation on Ubuntu requires installing Ruby and all the required libraries The following commands need to be executed in a terminal sudo credentials required EXTRACTING THE FORECASTER APPLICATION The first step is to uncompress the forecaster tgz tar gzip file into the folder of your choice Once the application is ready open a terminal and type the commands required for each step as described below INSTALLING RUBY Installing the required packages sudo aptitude install rubyl 8 dev rubyl 8 ril 8 rdocl 8 irb1 8 libreadline ruby1 8
8. sary IIBratles u uita br epo Lp REB EE PR Reo ObUr t RO A RU uri Rp Bean upniR 7 Running the ADDICSEOfIL eic ctp iiie oL batis db nonton a cmd en usan RUN aaa 7 Linux Centos 5 System Installation cortar hee A eR S pL Um Un Eran Lu Da EU RR tRe REND DEL RID UEA 8 Extracting the Forecaster application iniu d rore tbe RER E Le nb Ro eor Rab ERR CL B RR Cz ER Aun 8 Downloading and Installing Ruby tni Ur ton e tb ROB debe en Oba RUEDA RU Curio pU a ERR dui 8 installing RUBUBOTTIS cod eii pla mL ean a U E C arid t Ua MD 8 Installing the necessary libraries iie ire ette Uo Re aE 9 Running the Application sou essct ta Edo coia tito IAd eDeteased idee tpi etta tegis etc Pasi dett d edit 9 Linux Centos 6 System Installation eeseeessss sese eene eene nennen nnne enne 9 Extracting the Forecaster application cccsscccecssssececssseecececsseeececssuececsssaeeecssseeeeeeesenaes 9 Installing Rab uiieoipesseio te piod a ed roehnuR ven MGE URo fat sabiugeledenyadeddubigusaaelauidecad latechtitasndevbaes 10 Installing Rubygems iuto rne terii eh eei aai boi UR EIUS cedes nib Iteblqus ea olea i das Lus tO fusdd dubia uddeus 10 Installing the necessary libraries iicet tette einen ean aaa tnnt enn arn deu 10 Running the Application sis te eee eit e eni ee cre Troubleshooting Linux host Minimum System Requirements WINDOWS Windows XP Vista 7 or 8 32 or 64 bits architecture A 6 Gb of RAM memory
9. t 6 6 0 6 3600 Use CTRL C to stop Finally open your favorite browser and navigate to http 127 0 0 1 3000 and the login screen will appear The default user can login with login admin and password fitted The forecaster application can be reached from another computer connected to the network by using the IP address of the server ex http 168 192 0 11 3000 LINUX PORTABLE INSTALLATION Version recommended Linux 64 bits A Installation on Linux without any system installation is possible using the rubyportable package The location of the rubyportable folder needs to be opt rubyportable or configured using the setup sh script see below The following commands need to be executed in a terminal EXTRACTING THE FORECASTER APPLICATION The first step is to uncompress the forecaster tgz tar gzip file into the folder of your choice Once the application is ready open a terminal and type the commands required for each step as described below EXTRACTING THE RUBY PORTABLE APPLICATION The first step is to uncompress the rubyportable tgz file to the opt folder root required sudo su cd opt tar xvf rubyportable tgz exit Alternatively if you don t have root permission to the opt folder you can run the script setup sh to configure the ruby portable files according to your actual path root not required tar xvf rubyportable tgz sh setup sh cp start forecaster sh path to your FORECASTER insta

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