Lab IT: Difference between revisions

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Line 39: Line 39:
     mv LabNotes.v1.13.2/zhangloupload LabNotes
     mv LabNotes.v1.13.2/zhangloupload LabNotes
     apachectl start
     apachectl start
*[http://www.mediawiki.org/wiki/Extension:SphinxSearch|Sphinx 0.9.9 full text search engine] installed (Jan-23-2010)


==Genome-miner==
==Genome-miner==

Revision as of 07:27, 24 January 2010

NAS

  • Apple Time Capsule 877b54
    • MAC address: 00:1F:00:1F:5B:87:7B:54
    • Wireless password: Zhang lab's common password.
    • Backup of lab wiki, also serves as a wireless router.

Wiki server

  cd /etc/httpd/
  sudo htpasswd passwords new_user_name
  
  Edit the httpd.conf file.
  Add the new_user_name to the following line:
  Require user kunzhang ...some_existing_user_name
      • Wiki backup
  Launchd deamon:  /Library/LaunchDeamons/labwiki.backup
  Script for backup: /Library/Scripts/wiki_backup.sh
  • Server migration from Mac Mini to Mac Pro: Migration Log
  • Reads from genome-miner are shared in /Volumes/genome-miner-SeqStore2/ (See [1])
  • MediaWiki was upgrade from v 1.13.2 to v 1.15.1
    apachectl stop
    #backup the mysql databases
    mv LabNotes  LabNotes.v1.13.2
    tar -xzvf mediawiki-1.15.1.tar.gz
    mv mediawiki-1.15.1 LabNotes
    cp LabNotes.v1.13.2/LocalSettings.php LabNotes
    cp -r LabNotes.v1.13.2/extensions LabNotes
    cp /LabNotes/AdminSettings.sample /LabNotes/AdminSettings.php
    #edit the /LabNotes/AdminSettings.php file for the admin previlege
    cd LabNotes/maintenance
    php update.php --aconf ../AdminSettings.php
    cd ../..
    mv LabNotes.v1.13.2/upload LabNotes
    mv LabNotes.v1.13.2/zhangloupload LabNotes
    apachectl start

Genome-miner

  • A MacPro (8 core, 16GB RAM, 4TB), dedicated for GA Pipeline (PFBH406)
    • MAC addresses:
      • Port 1: 00:25:00:ee:6f:c8; connected to the campus network;
        • IP=132.239.135.41;
        • Subnet: 255.255.0.0
        • Gateway: 132.239.135.1
        • DNS: 132.239.0.252, 128.54.16.2
      • Port 2: 00:25:00:ee:3f:85; connected to GA PC;
        • IP=192.168.137.11
  • Installation of Ubuntu 9.04 (AMD64 Desktop).
    • Installed rEFIt for dual booting (http://refit.sourceforge.net/).
    • Installed Ubuntu 9.04 Desktop from ISO image.
      • Turned out that all the hard drives were not recognized with the RAID card. Removed the RAID card.
      • Press "c" to boot from the CD.
      • The OS was install in the hard drive in Bay 4.
      • The other two hard drives in Bay 2&3 were also reformatted to ext3
    • Ubuntu booted up correctly, but without network connection. Turned out that the Ethernet card was too new.
      • Downloaded the driver from sf.net/projects/e1000, manually changed the following two files, compiled and installed the driver.
   Added the following to the netdev.c: 
        {PCI_VDEVICE(INTEL, 0x10F6), board_82574}
   and to hw.h
        #define E1000_DEV_ID_82574L_NEW 0x10F6
  • Installed GA_pipeline 1.4
    • Install the Ubuntu Development Package:
     apt-get install build-essential
    • Installed fftw-3.2.1, need to compile with --enable-single;
    • Installed gnuplot;
    • Installed ImageMagik (for the convert function);
    • Installed zlib, bzlib2;
    • Install XML::Simple perl module.
    • Run make, all prerequisites passed.
    • Installed UNAFold (http://dinamelt.bioinfo.rpi.edu/) in /usr/local/

Printers

  • Brother HL-5250DN, PFBH406, attached to ZhangLab-GelDoc through USB. IP=132.239.25.45
  • Brother HL-4040CN, PFBH402, network printer, IP=172.16.25.87.
  • Brother MFC-7220, PFBH402, attached to Time Capsule through USB.

Share computers

  • ZhangLab-GelDoc, PC desktop, attached to the BioRad GelDocXL system.
    • IP: 132.239.25.45.
    • To map the shared data folder, use the network path: \\132.239.25.45\GelImages
  • ZhangLab-Chromo4, PC desktop, attached to Biorad Chromo4 Thermalcycler.
    • IP: 132.239.135.43.
    • To map the shared data folder, use the network path: \\132.239.135.43\Users
  • ZhangLab-VGN, PC laptop.