Lab IT: Difference between revisions
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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
- MacMini, Mac OS X,
- Hostname: genome-tech.ucsd.edu
- IP address: 132.239.25.34
- Public site: http://genome-tech.ucsd.edu/public
- Private wiki: http://genome-tech.ucsd.edu/LabNotes , password protected.
- How to add a new user:
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
- 0.9.9 full text search engine installed (Jan-23-2010)
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
- Port 1: 00:25:00:ee:6f:c8; connected to the campus network;
- MAC addresses:
- 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.
- 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.