ABySS denovo assembly installation

Question

[assembly.bfx1]

Hi Dr, Vandervalk,

I like to do my denovo assembly with your AByss tool, I have installed it, but I think there is a problem in configuration as I didn't see the PATH, so may be that is the reason I couldn't execute.

I got google sparsehash as directed to have the root privilege:

wget http://google-sparsehash.googlecode.com/files/sparsehash-1.11.tar.gz

and I unpacked. Then in sparsehash-1.11 dir I downloaded AByss:

wget http://www.bcgsc.ca/downloads/abyss/abyss-1.9.0.tar.gz

Although it was connected but as didn't get response, I just downloaded ABySS in my directory:

tar -zxf /home/mydir/abyss-1.9.0.tar.gz

and I unpacked, when I see abyss-1.9.0 in the dir

Next, I compiled by going to abyss-1.9.0 dir:

./configure && make
./configure CPPFLAGS=-I/usr/local/include
./configure --enable-maxk=96 && make

I can see my bin dir, and also in bin the abyss -pe, BUT I don't see PATH.

When I try to find 'abyss-pe version', I didn't see the PATH. That means I didn't configure ABySS properly, isn't it? I would appreciate if you could help me to install and compile the program properly, so that I can run my samples.

[Ram]

The URL for abyss-1.9.0 is https://github.com/bcgsc/abyss/releases/download/1.9.0/abyss-1.9.0.tar.gz - just FYI. Google would have helped there.

Answer 1

[Ram]

To add abyss to PATH, just run:

echo 'export PATH=$PATH:/home/mydir/abyss-1.9.0/bin'  >> ~/.bash_profile
source ~/.bash_profile

Also, the homepage has detailed instructions. Why not Google first? https://github.com/bcgsc/abyss#abyss

[h.mon]

sorry Ram, did not see your answer.

[Ram]

It was almost at the exact same time, no way either of us could've known:)

Answer 2

[h.mon]

You have to set PATH:

export PATH=/path/to/abyss:$PATH

You either use the command above each time you want to run abyss, or append it to your .bashrc file.