Installation of OSDDlinux on existing machines

This page is for linux users who wish to install software package or web servers of OSDDlinux on their existing machines. Most of packages are perl based so they may run on any machines with few customization. We have checked on RedHat,CentOS, Ubuntu, Scientific Linux and BOSS, here we have described customization steps for these operating system. Following is description of installation of OSDDlinux on major machines


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Pre installation setup for all type of machines
In order to install OSDDlinux on existing machines, user should follow steps given below.
  • Make a directory "/gpsr/" (directory for installing osddlinux, mkdir /gpsr )
  • Create a account name "gpsr" with home directory "/gpsr/" (useradd -d /gpsr gpsr)
  • Login to system as user "gpsr"
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    Installation on Ubuntu 64bit

    1. First user need to download following files to directory "/gpsr/"
    2. Uncompress and detar above files in directory "/gpsr" (e.g., tar -zxvf base.tar.gz)
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    Installation on Ubuntu 32bit

    1. First user need to download following files to directory "/gpsr/"
    2. Uncompress and detar above files in directory "/gpsr" (e.g., tar -zxvf base.tar.gz)
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    Installation on Mac OSX

    Preinstallation Steps
    • Make a directory "/gpsr/" (directory for installing OSDDlinux, "mkdir /gpsr")
    • Create a account name "gpsr" with home directory "/gpsr/" (If you don't have enough space in root directory (i.e. / ), then click here to follow steps)
      NOTE: By default, home directory of newly created account is made in "/Users/" directory. To change it, go to "System Preferences" and then to "Users & Groups". Now right click on newly created gpsr account and click on "Advanced Options..." and change the home directory to "/gpsr". Now using root previledges type this command (mv /Users/gpsr /gpsr) to shift home directory of gpsr account to "/gpsr"
    • Login to system as "gpsr"
    Installation Steps
    1. First user need to download following files to directory "/gpsr/"
    2. Uncompress and detar above files in directory "/gpsr" (e.g., tar -zxvf base.tar.gz)
    Postinstallation steps
    • Type following command ("cat /gpsr/gpsr_env.sh >> /gpsr/.bash_profile") to include path variables
    • Change ownership of files in /gpsr ("chown -R gpsr /gpsr/*")
    • Change group of all files in /gpsr ("chgrp -R gpsr /gpsr/*")
    • Start crontab jobs to excute background jobs ("crontab /gpsr/cronjobs")
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    Redhat 64 bit installation instructions

    1. First user need to download following files to directory "/gpsr/"
    2. Uncompress and detar above files in directory "/gpsr" (e.g., tar -zxvf base.tar.gz
    3. Installing essential packages
      • Login as super user
      • update yum
      • yum install httpd
      • yum install php (install all libraries)
      • yum install phython
    4. Configure apache/httpd
      • Edit /etc/httpd/conf/httpd.conf
        • Listen:8000
        • User gpsr
        • Group gpsr
        • DocumentRoot /gpsr/webserver/cgidocs
        • Directory /gpsr/webserver/cgidocs
        • ScriptAlias /cgi-bin/ "/gpsr/webserver/cgibin/"
        • ScriptAlias /cgibin/ "/gpsr/webserver/cgibin/"
        • Directory "/gpsr/webserver/cgibin"
      • setsebool -P httpd_enable_homedirs true
      • chcon -R -t httpd_sys_content_t /gpsr/webserver/*

    5. Start Web Server (/sbin/service httpd start)
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    Fedora 64 bit installation instructions

    1. First user need to download following files to directory "/gpsr/"
    2. Uncompress and detar above files in directory "/gpsr" (e.g., tar -zxvf base.tar.gz
    3. Installing essential packages
      • Login as super user
      • update yum
      • yum install httpd
      • yum install php (install all libraries)
      • yum install phython
    4. Configure apache/httpd
      • Edit /etc/httpd/conf/httpd.conf
        • Listen:8000
        • User gpsr
        • Group gpsr
        • DocumentRoot /gpsr/webserver/cgidocs
        • Directory /gpsr/webserver/cgidocs
        • ScriptAlias /cgi-bin/ "/gpsr/webserver/cgibin/"
        • ScriptAlias /cgibin/ "/gpsr/webserver/cgibin/"
        • Directory "/gpsr/webserver/cgibin"
      • setsebool -P httpd_enable_homedirs true
      • chcon -R -t httpd_sys_content_t /gpsr/webserver/*

    5. Start Web Server (service httpd start)
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    Installation on CentOS
    1. First user need to download following files to directory "/gpsr/"
    2. Uncompress and detar above files in directory "/gpsr" (e.g., tar -zxvf base.tar.gz
    3. Installing essential packages
      • Login as super user
      • Install repoforge on Centos using rpm from RPMForge
      • update yum
      • yum install httpd httpd-devel httpd-tools
      • yum install php php-mysql (install all libraries)
      • yum install phython
      • updatedb
      • yum install mhash-devel.x86_64
      • yum libmcrypt.x86_64
      • yum install dos2unix
      • yum install tcsh
      • yum install R
      • yum install babel
      • yum install java
      • yum install perl-GD
    4. Configure apache/httpd
      • Edit /etc/httpd/conf/httpd_conf
        • Listen:8000
        • User gpsr
        • Group gpsr
        • DocumentRoot /gpsr/webserver/cgidocs
        • Directory /gpsr/webserver/cgidocs
        • ScriptAlias /cgi-bin/ "/gpsr/webserver/cgibin/"
        • ScriptAlias /cgibin/ "/gpsr/webserver/cgibin/"
        • Directory "/gpsr/webserver/cgibin"
      • Allowing httpd accessing home directories
        • # setsebool -P httpd_enable_homedirs true
        • # chcon -R -t httpd_sys_content_t /gpsr/webserver/*
    5. Edit file /etc/selinux/config (change the status from "enforcing" to "disabled")
    6. Start Web Server (service httpd start)
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    Installation on Scientific Linux
    1. First user need to download following files to directory "/gpsr/"
    2. Uncompress and detar above files in directory "/gpsr" (e.g., tar -zxvf base.tar.gz
    3. Installing essential packages
      • Login as super user
      • update yum
      • yum install httpd httpd-devel httpd-tools
      • yum install php php-mysql (install all libraries)
      • yum install phython
      • updatedb
      • yum install mhash-devel.x86_64
      • yum libmcrypt.x86_64
      • yum install dos2unix
      • yum install tcsh
      • yum install R
      • yum install babel
      • yum install java
      • yum install perl-GD
    4. Configure apache/httpd
      • Edit /etc/httpd/conf/httpd_conf
        • Listen:8000
        • User gpsr
        • Group gpsr
        • DocumentRoot /gpsr/webserver/cgidocs
        • Directory /gpsr/webserver/cgidocs
        • ScriptAlias /cgi-bin/ "/gpsr/webserver/cgibin/"
        • ScriptAlias /cgibin/ "/gpsr/webserver/cgibin/"
        • Directory "/gpsr/webserver/cgibin"
      • Allowing httpd accessing home directories
        • # setsebool -P httpd_enable_homedirs true
        • # chcon -R -t httpd_sys_content_t /gpsr/webserver/*
    5. Edit file /etc/selinux/config (change the status from "enforcing" to "disabled")
    6. Start Web Server (service httpd start)
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    Installation on Bharat Operating System Solutions (BOSS)

    1. First user need to download following files to directory "/gpsr/"
    2. Uncompress and detar above files in directory "/gpsr" (e.g., tar -zxvf base.tar.gz)
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    Installation on any unix based machine

    1. First user need to download following files to directory "/gpsr/"
    2. Uncompress and detar above files in directory "/gpsr" (e.g., tar -zxvf base.tar.gz)
    3. Set the environment paths by following command ("cat /gpsr/gpsr_env.sh >> ~/.bashrc")
    4. Set the crontab jobs by following command ("crontab /gpsr/cronjobs")

      Configuring Standalones in /gpsr/standalone
    5. Most of the standalone programs in /gpsr/standalone directory are simply perl based. As all codes are having path from /gpsr/local/bin/perl, type following command to copy perl of system by following command ("cp /usr/bin/perl /gpsr/local/bin/")
    6. For installation of GD module in perl (required by softwares like propred), go to cpan by typing following command ("cpan") and while in cpan, type following command ("install GD"). This will install GD module for perl. NOTE: If you are using cpan for the first time, it will ask you some questions to configure cpan. You can accept default settings and proceed.
    7. Some of the standalone are having c programs which needs to be recompiled to run. These standalones are abcpred, alphapred, ar_nhpred, betatpred2, betaturns, chpredict, ctlpred, gammapred, nhlapred, sarpred, tbbpred, hladr4pred. Go to progs directory of each standalone and type following command ("make") in that directory. (e.g. "cd /gpsr/standalone/abcpred/progs/" followed by "make")
      "cd /gpsr/standalone/alphapred/progs/" followed by "make"
      "cd /gpsr/standalone/ar_nhpred/progs/" followed by "make"
      "cd /gpsr/standalone/betatpred2/progs/" followed by "make"
      "cd /gpsr/standalone/betaturns/progs/" followed by "make"
      "cd /gpsr/standalone/chpredict/progs/" followed by "make"
      "cd /gpsr/standalone/ctlpred/progs/" followed by "make"
      "cd /gpsr/standalone/gammapred/progs/" followed by "make"
      "cd /gpsr/standalone/nhlapred/progs/" followed by "make"
      "cd /gpsr/standalone/sarpred/progs/" followed by "make"
      "cd /gpsr/standalone/tbbpred/progs/" followed by "make"
      "cd /gpsr/standalone/hladr4pred/progs/" followed by "make"
    8. To recompile meme/mast software which is required by some packages, type following commands ("cd /gpsr/software/meme/") and then ("../meme.conf") then type ("make") and finally ("make install"). It will install meme/mast software. It will also install readseq software required by many standalone packages.
    9. You also need to download latest blast binaries as per your machine architecture from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/ and put in following path "/gpsr/software/blastpr/"
    10. You also need to compile psipred software (which is for protein secondary structure prediction) and put it in following path "/gpsr/software/psipred2/"

      Configuring Webservers in /gpsr/webserver
    11. Webservices in /gpsr have 2 main directories. (a) /gpsr/webserver/cgidocs which is Document Root i.e. webservices are launched from this directory. Anything kept in this directory will be available to the public via web. (b) /gpsr/webserver/cgibin in which all scripts of software packages are available.
      To use webservices of /gpsr, you need to install apache2 server software and need to do following changes in it.
      • Edit configuration file of apache2 (/etc/apache2/httpd.conf)
        • Listen:8000
        • User gpsr
        • Group gpsr
        • DocumentRoot /gpsr/webserver/cgidocs
        • Directory /gpsr/webserver/cgidocs
        • Alias /raghava "/gpsr/webserver/cgidocs/raghava"
        • Alias /tmp "/gpsr/webserver/cgidocs/tmp"
        • ScriptAlias /cgi-bin/ "/gpsr/webserver/cgibin/"
        • ScriptAlias /cgibin/ "/gpsr/webserver/cgibin/"
        • Directory "/gpsr/webserver/cgibin"
      • Start the webserver ("service httpd start"). Now you can access the webservers at http://localhost:8000/raghava/


      Configuring Galaxy in /gpsr/galaxy
    12. Galaxy is an open source web based platform for data intensive work. Galaxy is compatible with Python Version 2.6 and 2.7. Therefore we need to compile latest python in /gpsr/local/bin.
      • To configure latest python, go to /gpsr/source/Python/ by command ("cd /gpsr/source/Python/") and then type this command ("../python.conf"). It will configure Python. Now type command ("make") and finally ("make install") to install latest Python.
      • Now go to /gpsr/galaxy by command ("cd /gpsr/galaxy") and run following command ("sh run.sh"). It will download system specific python eggs which are required for Galaxy to run.
      • After it has downloaded eggs successfully, you can use Galaxy resources via http://localhost:8001
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    Post installation for all machines
    1. Change ownership of files in /gpsr ("chown -R gpsr /gpsr/*")
    2. Change group of all files in /gpsr ("chgrp -R gpsr /gpsr/*")
    3. Start crontab jobs to excute background jobs ("crontab /gpsr/cronjobs")
    4. Restart your computer
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    Troubleshooting or Alternatives This section is for providing important information on critical issues
    1. Harddisk Space
      OSDDlinux required 10 GB or more space on hardisk, In case you do not have sufficient space, you may use one of the following alternates
      • Soft Link: You may load OSDDlinux files in any directory (e.g. /usr1/gpsr ), link this directory with "/gpsr" using following command
        ln -s /usr1/gpsr /gpsr
      • Bind Directory: You may copy files in any directory (e.g. /usr1/gpsr), mount this directory to /gpsr , using following command
        mount -bind /usr1/gpsr /gpsr
        Add following entry in "/etc/fstab" file, "/usr1/gpsr   /gpsr   none   bind"
      • Mount Disk: If you wants to install on a hardisk volume or on external hardisk or on removable media (e.g., USB,DVD), you mount it to "/gpsr". Make entry in fstab for permanent mounting.
    2. Rsync Facility
      In case your Internet is slow or not relable for long duration, it will be difficult to download tar files as size of files is huge. You may copy OSDDlinux files using following command for different machines, these commands may be used for updation or syncronization of files
      • Ubuntu
        rsync -avz osddlinux.osdd.net::osddlinux/ubuntu/64bit/base/* /gpsr/. (Base Infrastructure)
        rsync -avz osddlinux.osdd.net::osddlinux/ubuntu/64bit/packages/* /gpsr/. (Additional Packages)
      • Mac OSX
        rsync -avz osddlinux.osdd.net::osddlinux/macosx/64bit/base/* /gpsr/. (Base Infrastructure)
        rsync -avz osddlinux.osdd.net::osddlinux/macosx/64bit/packages/* /gpsr/. (Additional Packages)
      • Fedora
        rsync -avz osddlinux.osdd.net::osddlinux/fedora/64bit/base/* /gpsr/. (Base Infrastructure)
        rsync -avz osddlinux.osdd.net::osddlinux/fedora/64bit/packages/* /gpsr/. (Additional Packages)
      • CentOS
        rsync -avz osddlinux.osdd.net::osddlinux/centos/64bit/base/* /gpsr/. (Base Infrastructure)
        rsync -avz osddlinux.osdd.net::osddlinux/centos/64bit/packages/* /gpsr/. (Additional Packages)
      • RedHat
        rsync -avz osddlinux.osdd.net::osddlinux/redhat/64bit/base/* /gpsr/. (Base Infrastructure)
        rsync -avz osddlinux.osdd.net::osddlinux/redhat/64bit/packages/* /gpsr/. (Additional Packages)
      • Scientific Linux
        rsync -avz osddlinux.osdd.net::osddlinux/scl/64bit/base/* /gpsr/. (Base Infrastructure)
        rsync -avz osddlinux.osdd.net::osddlinux/scl/64bit/packages/* /gpsr/. (Additional Packages)
    3. Internet Connectivity
      In order to install additional packages or libraries you need to set your Internet connecvtion. It may be direct via default router or set proxy environment to user Internet.
    4. OSDDlinux Modules In case user is not interested in installing whole OSDDlinux and wish to install only selectd moduless. User may install individual packages as per requirement after installing base or minimum structure.
    5. OSDDlinux Modules A user can install specific module (Bioinformatics module, Vaccine-informatics module, Drug informatics module etc) using their respective deb files, on his/her existing machine provided he/she has already installed OSDDlinux base architecture. User may download a package from repository of packages
      . Run follwoing command to install a specific package (after downloading from repository) "dpkg -i example.deb".