Installing ARB in Ubuntu Hardy LTS

How to install ARB on Ubuntu Hardy LTS.  These are my notes of what worked on my system, and depending on what you already have installed, you may have additional requirements.  (Please feel free to make note of your experience in the comments, if you’d like to share!) This is a modified copy from my previous post for installing in Feisty Fawn.

Make sure you have the prerequisite packages installed:

• transfig
• xfig
• xviewg
• gv
• libmotif3

Download the latest ARB for linux at www.arb-home.de.  The download directory contains three files; you need to put all of them in the same place: arb_install.sh, arb.tgz and zcat. No need to untar anything.

In the directory where you put these downloads,

$ sudo sh arb_install.sh

The script asks a bunch of installation questions, and it’s pretty self-explanatory about what it’s asking, so go nuts.  I used all the defaults for a stand-alone computer, except I used /opt/arb as the install directory instead of /usr/arb.

When the script exits, it mentions editing something in /etc (but it doesn’t say what).  In Feisty, you need to add the following lines to the /etc/bash.bashrc file (assuming you used /opt/arb as the installation directory like me–otherwise, you may have to replace “opt” below with “usr”):

ARBHOME=/opt/arb;export ARBHOME
LD_LIBRARY_PATH=${ARBHOME}/lib:${LD_LIBRARY_PATH}
export LD_LIBRARY_PATH
PATH=${ARBHOME}/bin:${PATH}
export PATH
alias arb=/opt/arb/bin/arb
echo “This shell is ARB-enabled.”  #Not necessary.  Just for fun.

It now seems to work!  You can delete the installation files.  Or, you can change your current installation by running arb_install.sh again.

howto: install ARB in Ubuntu Feisty

Make sure you have the prerequisites (most notably, in Feisty, the libstdc++2.10-glibc2.2 package, which I had to do some digging to figure out):

• transfig
• xfig
• xviewg
• gv
• libstdc++2.10-glibc2.2 (in the universe repository)

Download the latest ARB for linux at www.arb-home.de.  The download directory contains three files; you need to put all of them in the same place: arb_install.sh, arb.tgz and zcat. No need to untar anything.

In the directory where you put these downloads,

$ sudo sh arb_install.sh

The script asks a bunch of installation questions, and it’s pretty self-explanatory about what it’s asking, so go nuts.  I used all the defaults for a stand-alone computer, except I used /opt/arb as the install directory instead of /usr/arb.

When the script exits, it mentions editing something in /etc (but it doesn’t say what).  In Feisty, you need to add the following lines to the /etc/bash.bashrc file (assuming you used /opt/arb as the installation directory like me–otherwise, you may have to replace “opt” below with “usr”):

ARBHOME=/opt/arb;export ARBHOME
LD_LIBRARY_PATH=${ARBHOME}/lib:${LD_LIBRARY_PATH}
export LD_LIBRARY_PATH
PATH=${ARBHOME}/bin:${PATH}
export PATH
alias arb=/opt/arb/bin/arb
echo “This shell is ARB-enabled.”  #Not necessary.  Just for fun.

It now seems to work!  You can delete the installation files.  Or, you can change your current installation by running arb_install.sh again.

howto BLAST

In ubuntu, the BLAST package is called blast2

sudo aptitude install blast2

This installs a whole bunch of blast commands for local and remote searching.  For example, you can search NCBI with a list of fasta entries as queries (sequentially) using the remote NCBI server to do the work:

blastcl3 -p blastp -m 3 -v 10 -b 10 -i infile.fasta -o outfile.txt

Where, here I’m just looking for a few quick top hits.  -p is the important option, where you define the search engine.  In this example I’m using blastp to search protein.  I think the default database is ncbi nr.

And here’s an example of searching a local database using your own cpu:

blast2 -p blastp -m 3 -v 10 -b 10 -i infile.fasta

and an outfile isn’t defined, so it just goes to standard out, ready for pipes.