I have switched jobs! still doing bioinformatics but for a service company providing next gen sequencing. Hence I think I shall move to a new blog address its here at http://kevin-gattaca.blogspot.com/ if its still relevant to you
installed gnome-do and avant-window-navigator
trying to figure compositing.. hmm good that metacity does compositing!
The quirks of my spanking new Ubuntu install is driving me nuts..
I found solutions online that do not seem to work!
1) I have to alt-tab twice to change windows (the first just shows the popup)
but it seems that using compositing or adding visual effects solves the problem!
2) Alt_R doesn’t work! its a special mod key but xmodmap doesn’t help!
Any solutions is appreciated!
Finally made the move!
My old version was no longer supported (read respository servers are gone!)
I needed a bit of house cleaing (read I have files which i have no use for and don’t know if i shld del)
so the move was needed.
I wanted to use LTS (long term support)
but by a twist of fate i ended up with 9.04 amd64 no less (to make use of the 16gb ram that i got)
I must say the upgrade IS an upgrade. the graphics are slicker and more imptly they are faster!
the migration went well. So far I didn’t have to recustomize most of my settings. Just copying the profiles sorted everything.
but have the usual hiccups of having to reinstalling
- sun java 6
- flock-browser (why can’t i just copy it over?? had to get the deb from http://www.getdeb.net/)
- gnome-vim (why doesn’t this ship with ubuntu as default?)
- 64bit flash player (hmm haven’t gotten down to this yet)
But I must say the advantages are
- better support for HP network printers (yeah! no more manual setups with IP addresses)
- Google-chrome works!
- did I mention again that its faster and slicker?
after looking at gOS I might even fiddle to get a Mac look just to be the envy of my less techy frens
so far I haven’t met a prob like nsaunders.. with upgraded packages but will keep a note for his method
Wished I could have been there.. would love to c what tools are lacking for next gen seq technologies.
Had to use bash to run a few one off jobs or edit my bash_profile for enviroment settings..
these are useful links!
http://www.linux.com/feature/155903 — Patterns and string processing in shell scripts
http://www.linux.com/feature/147568 — Save time at the command line with shell aliases and functions
Get it while its hot! :)
will post experiences on an Ubuntu box later
The problem that needed solving this time was having a list of filenames of my ab1 files, location( directory path) and a md5sum so i know if duplicate filenames are the same file or just a result of misnaming.
managed to come up with this after copying from two different scripts
one that was used to make an inventory of a directory of ogg songs and the other a python equivalent of md5sum check in linux.
#!/usr/bin/python #=============================================================================== # # FILE: inventory-abi.py # # USAGE: ./inventory-abi.py # # DESCRIPTION: Lists all the files of extension .ab1 with the directory and its md5sum # adapated from code from http://pthree.org/2007/08/09/recursion-in-python/ and # used md5sum code from http://code.activestate.com/recipes/266486/ # OPTIONS: --- # REQUIREMENTS: --- # BUGS: will execute md5 on directory as well # current method to get CWD is not OS independent # NOTES: --- # AUTHOR: Kevin , # VERSION: 1.0 # CREATED: 11/07/2008 07:03:16 PM SGT # REVISION: --- #=============================================================================== import dircache, os, md5 counter = 0 def sumfile(fobj): '''Returns an md5 hash for an object with read() method.''' m = md5.new() while True: d = fobj.read(8096) if not d: break m.update(d) return m.hexdigest() def md5sum(fname): '''Returns an md5 hash for file fname, or stdin if fname is "-".''' if fname == '-': ret = sumfile(sys.stdin) else: try: f = file(fname, 'rb') except: return 'Failed to open file' ret = sumfile(f) f.close() return ret def PrintFiles(indent): global counter thisDir = os.getcwd() for file in dircache.listdir(thisDir): if (file.endswith('ab1') or os.path.isdir(file)) and not file.startswith('.'): if file.endswith('ab1'): counter += 1 currdir = os.popen("pwd") #for output of cwd currently works for linux pending upgrade to OS independent md5 = md5sum(file) #calls the md5sum function, md5 lib ships with Python ab1File.write('%s%s\t%s\t%s\n' %(indent, file, currdir.readline()[:-1], md5)) if os.path.isdir(file): os.chdir(file) PrintFiles(indent + ' ') os.chdir('../') try: ab1File = open('ab1files.txt', 'w') except IOError, e: print "Unable to open 'ab1files.txt' for writing: ", e else: PrintFiles('') ab1File.write('\nCurrent number of ab1 files: %d\n\n' %(counter)) ab1File.close()
Lolz writing now from the Google DevFest at Singapore… hmm sadly its not packed to the brim right now.. maybe cos its just after a long weekend. oh well, am pretty excited though.. will post relevant updates if any..
my online notes as the event progresses
Update: There’s going to be a SE Asia OpenSocial Application Contest
Check out details at http://code.google.com/events/apacdevfest/contest/
The Event website