Category: "Unix"

Lucene Search

June 11th, 2009
To use the Lucene search engine for querying the GenTrack system, an XML dump must be prepared. This should be done daily to allow a regular re-indexing of the search. We are indexing on the gene and transcript level separately. The XML can be written… more »

FTP at the Sanger Institute

June 8th, 2009
To updload data to the Sanger FTP server: Using an ftp program, connect to ftp.sanger.ac.uk Anonymous logins are possible. Change into the pub/incoming directory Transfer the files. Disconnect 20 minutes after the file has been untouched, it will be… more »

Unix Process Information

May 14th, 2009
To find out more about processes running on your machine you can: top for specific process look into the process's data in /proc eg. more »

Grep

December 2nd, 2008
Some useful option for the unix command grep just COUNT occurrences: grep -c find text.txt using NOT: grep -v notfind text.txt ignore the case: grep -i UPorLOW text.txt using OR: egrep 'this|that' text.txt show context: also show… more »

Sanger Web-Proxy

November 20th, 2008
If you work at the Welcome Trust Sanger Institute and would like to browse web pages at home the same way you do at work, here is how to set it up: You need an ssh login, open a terminal window and connect like this ssh -L3128:webcache.sanger.ac.… more »