Monday, June 23, 2008

base64 decode

I was playing around with launching the taverna workflow engine programmatically. The answers it spat back out all looked slightly weird.

IyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIwojIFByb2dyYW06IGFudGln
ZW5pYwojIFJ1bmRhdGU6IFRodSAxOSBKdW4gMjAwOCAxMjoyNDo0MgojIENvbW1hbmRsaW5lOiBh
bnRpZ2VuaWMKIyAgICAtc2VxdWVuY2Ugc3dpc3Nwcm90OlAwNDYzNwojICAgIC1vdXRmaWxlICIv
ZWJpL2V4dHNlcnYvc29hcGxhYi13b3JrL3NvYXBsYWIyX2VtYm9zczQvU0FOREJPWC9bcHJvdGVp
bl9tb3RpZnMuYW50aWdlbmljXS0yNTc4NTMyNi


According to the taverna user group this is cos the answer is encoded in base64. To see how it should look, stick it through mmencode:
mmencode -u name.txt

A somewhat more comprehensable answer should emerge:
########################################
# Program: antigenic
# Rundate: Thu 19 Jun 2008 12:24:42
# Commandline: antigenic
# -sequence swissprot:P04637
# -outfile "/ebi/extserv/soaplab-work/soaplab2_emboss4/SANDBOX/[protein_motifs.antigenic]-25785326.11a9e381fc5.67f8/o_outfile"
# -auto
# Report_format: motif
# Report_file: /ebi/extserv/soaplab-work/soaplab2_emboss4/SANDBOX/[protein_motifs.antigenic]-25785326.11a9e381fc5.67f8/o_outfile
########################################

#=======================================
#
# Sequence: P53_HUMAN from: 1 to: 393
# HitCount: 15
#=======================================



Now to find the java libraries to do this in code.

Saturday, June 21, 2008

Vim C++ Autocompletion

Download and install vimcppomnicomplete: http://www.vim.org/scripts/script.php?script_id=1520


Install ctags (not the Emacs version): http://ctags.sourceforge.net/

In /usr/include type:

ctags -f ~/.vim/stdtags -R --c++-kinds=+p --fields=+iaS --extra=+q .



Add the following to ~/.vimrc:


set nocp
filetype plugin on
map <C-L> :!ctags -R --c++-kinds=+p --fields=+iaS --extra=+q .<CR><CR>

set tags=~/.vim/stdtags,tags,.tags,../tags

autocmd InsertLeave * if pumvisible() == 0|pclose|endif


The final line closes the completion box when you leave insert mode. Ctrl-L will update the tags (and so let you autocomplete based on new files) files in the current directory. Thanks go to the various places on the interwebs I robs this info from.

Thursday, June 12, 2008

Truecrypt commands

Given that I will probably forget all this I thought it best to write it down.

Create the volume:
truecrypt --create test.tc 


Mount that volume:
truecrypt test.tc /mnt/data/


Unmount it:
truecrypt --dismount test.tc


All stolen from here:
http://www.movingtofreedom.org/2007/02/10/truecrypt-in-ubuntu-and-fedora-gnu-linux/