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Dinh:Genome Miner Upgrades
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===Final configurations on Ubuntu 14.04=== * Run updates: sudo apt-get update * Install current nVidia drivers sudo apt-get install nvidia-current-updates * Install vim sudo apt-get install vim * Install ssh, the client should be already installed but run apt-get to make sure. sudo apt-get install openssh-client sudo apt-get install openssh-server * Install antivirus sudo apt-get install clamav clamav-daemon clamav-freshclam sudo freshclam sudo /etc/init.d/clamav-daemon start * Install gparted sudo apt-get install gparted * The RAID enclosures need gparted to be mounted. Use Athurva's tips on how to mount them. * Make the directories for mounting the three other Hitachi 2TB drives: sudo mkdir /media/TmpStore1 sudo mkdir /media/TmpStore2 sudo mkdir /media/FreshReads * Mount the three other Hitachi drives by copying these lines into /etc/fstab: UUID=aab32527-c79a-4c42-b5e1-6dac0d5fa104 /media/TmpStore1 ext3 user,exec 0 0 UUID=cdd8e7e8-ae10-49f8-bb0d-4a226cf9f255 /media/TmpStore2 ext3 user,exec 0 0 UUID=33a12e29-91f2-41dc-a441-d0d526f740e5 /media/FreshReads ext3 defaults,exec 0 0 * Run mount all command: sudo mount -a * Mount the previous root drive on an external enclosure, and copy over all user home directories to /home. * The three Synology diskstation folders need to be mounted. Make sure all users and groups are set up correctly. Then use Athurva's tips on how to mount them ** Genome-miner's local connection to the NetGear router via port number 2 needs to have an IP address set up manually to be able to connect to the Synology. *** Set up the IPv4 IP as 192.168.137.11 *** subnet mask as 255.255.255.0 *** leave Gateway address empty ** smbmount command is not available, used mount -t cifs (options for this command are the same). * Set up firewall sudo ufw enable sudo ufw allow ssh sudo ufw allow www sudo ufw allow ftp sudo ufw allow Samba sudo ufw reload * Install other services #sudo apt-get install build-essentials #sudo apt-get install gnuplot #sudo apt-get install fftw-dev #sudo apt-get install imagemagick --fix-missing #sudo apt-get install gambas3-gb-compress-bzlib2 #sudo apt-get install nfs-server #sudo apt-get install mysql-server #(root password is genomeclub) #sudo apt-get install gdm #(default display set as gdm) #sudo apt-get install lm-sensors #sudo apt-get install irqbalance #sudo apt-get install fancontrol #sudo apt-get install bootlogd #sudo apt-get install binfmt-support #sudo apt-get install pcmciautil #sudo apt-get install cifs-utils #sudo apt-get install sysfsutils #sudo apt-get install samba #sudo apt-get install portmap #(Note, selecting rpcbind instead of portmap) #sudo apt-get install screen #sudo apt-get install r-base-core #sudo apt-get install libffi-dev libssl-dev #for pysam * mysql database still need to be ported over. need to figure out how to do this. * copy over files in /opt #sudo cp -r /media/ddiep/79163ff1-f258-4fd7-8d1a-ce0ef71fa14e/opt/* /opt/ * Install perl modules CPAN, install XML::Simple, install File::Temp, install Sort::Array * Install unafoldv3.8 * Install R packages using list of packages saved from old server * Install mac applications: sudo add-apt-repository ppa:mactel-support/ppa sudo apt-get update sudo apt-get install macfanctld * Edit and copy over user accounts and group information #dir="/media/dinh/79163ff1-f258-4fd7-8d1a-ce0ef71fa14e" #awk -v LIMIT=1000 -F: '($3>=LIMIT) && ($3!=65534)' $dir/etc/passwd > passwd.sync #awk -v LIMIT=1000 -F: '($3>=LIMIT) && ($3!=65534)' $dir/etc/group > group.sync #awk -v LIMIT=1000 -F: '($3>=LIMIT) && ($3!=35534) {print $1}' $dir/etc/passwd | tee - | sudo egrep -f - $dir/etc/shadow > shadow.sync #awk -v LIMIT=1000 -F: '($3>=LIMIT) && ($3!=65534) {print $1}' $dir/etc/group | tee - | sudo egrep -f - $dir/etc/gshadow > gshadow.sync * Change ajgore uid to 1005 and delete entries for dinh * Port over user accounts: #cat passwd.sync >> /etc/passwd #cat group.sync >> /etc/group #cat shadow.sync >> /etc/shadow #cat gshadow.sync >> /etc/gshadow * Since all the uid and gid are maintained for most people, just need to run chown on Athurva's and Dinh's folders.
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