Count chars

We might have had this one before but I couldn't find it.

cat commafile.txt | tr -dc ',' | wc -c

That could be replaced by any file in the commfile.txt. So, basically count the number of occurrences of the expression ',' in the file and print it out. Why? you ask - cos I gotta.

Remote SVN access for Sanger Institute

As usually this config is ripped from various parts of the web, but it allows me to remotely access the SVN at the Sanger Institute. Place this configuration in ~/.ssh/config:

Host sangerTunnel
    HostName ssh.sanger.ac.uk
    Port 22

    # Subversion Server
    LocalForward localhost:2222  svn:22

###Hostname alias directives###
#These allow you to mimic hostnames as they appear at work.
#We just take the localhost names from the above section and add alias names.
#Note that you don't need to use a FQDN; you can use a short name ,such as smtp instead of smtp.pretendco.com.

Host svn.internal.sanger.ac.uk
    HostName localhost
    User YOURUSERNAME
    Port 2222
#End Config File

Then type:

ssh -v sangerTunnel -lYOURUSERNAME

to setup the tunnel. You will need to login (and connect to a host). You can then checkout your files, as if you were connected to the local network.

Here is the same for EMBL (couldn't correctly formatted code to comment):
I wanted to do the same to access my machine in EMBL. Here is how.

Host emblTunnel
    HostName ssh-proxy.embl.de
    Port 22

    # Subversion Server
    LocalForward localhost:2222 svn:22

###Hostname alias directives###
#These allow you to mimic hostnames as they appear at work.
#We just take the localhost names from the above section and add alias names.
#Note that you don't need to use a FQDN; you can use a short name ,such as smtp instead of smtp.pretendco.com.
Host mymachine
  HostName localhost
  Port 2222
  HostKeyAlias mymachine
  User nobodycares

You then type:

ssh emblTunnel

And then:

ssh mymachine

And then it shoudl be possible to scp stuff using scp mymachine:/path/to/file

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.

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.

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/

Using fetchmail with Exchange at the Wellcome Trust Sanger Institute

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