installing ABYSS using cygwin

Question

[reza]

hi

i am trying to install ABYSS using cygwin. i downloaded ABYSS, boost, openmpi, sqlite and sparsehash. all programs is in /cygdrive/c/users/rain/desktop directory in my PC. i am confuse about installing ABYSS. please help me to do it.

Answer 1

[benv]

I wouldn't recommend trying to run ABySS on cygwin -- I've never tested it and it's not a platform that we officially support. You will have far less problems on Linux/Mac, and I think you will find the story is the same for the majority of bioinformatics software. If you are really set on using Windows as your O/S then I would recommend setting up a virtual machine running Linux (e.g. Ubuntu) with VirtualBox or VMWare instead of using cygwin.

That said, if you want to try installing ABySS on cygwin anyway:

1. download the source tarball here: http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.0.0
2. unpack it: run tar xvf abyss-2.0.0.tar.gz in the download directory.
3. cd abyss-2.0.0
4. ./configure
5. make
6. make install

See https://github.com/bcgsc/abyss#compiling-abyss-from-source for more info.

Good luck!

[reza]

mentioned way to running ABYSS not worked. i checked above commands previously.

[benv]

Fair enough. I will need you to provide some more detailed information before I can help, though. At what step did the commands fail? What was the error message? Was there partial output from the failed command?

Answer 2

[Charles Warden]

I agree with benv. I would recommend either setting up a VirtualBox VM (where you can have an Unbuntu graphical interface).

https://www.virtualbox.org/wiki/Downloads

http://www.ubuntu.com/download/desktop

Installing Docker might also be a good option, where some other programs are even "Dockerized" (where you can download an image with the program already installed)

https://www.docker.com/products/docker-toolbox

https://docs.docker.com/engine/getstarted/