Question: installing ABYSS using cygwin
0
gravatar for reza
2.6 years ago by
reza210
Iran
reza210 wrote:

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.

abyss assembly • 844 views
ADD COMMENTlink modified 2.6 years ago by Charles Warden6.5k • written 2.6 years ago by reza210
1
gravatar for benv
2.6 years ago by
benv710
Canada
benv710 wrote:

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!

ADD COMMENTlink written 2.6 years ago by benv710

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

ADD REPLYlink written 2.6 years ago by reza210

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?

ADD REPLYlink written 2.6 years ago by benv710
0
gravatar for Charles Warden
2.6 years ago by
Charles Warden6.5k
Duarte, CA
Charles Warden6.5k wrote:

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/

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Charles Warden6.5k
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