abyss-fac: command not found on Kubuntu 14.04

Question

[Chip]

I installed ABySS following the instructions from the official documentation.

>sudo apt-get install abyss

and then proceeded with a simple test

>wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.3.4/test-data.tar.gz
>tar xzvf test-data.tar.gz
>abyss-pe k=25 name=test in='test-data/reads1.fastq test-data/reads2.fastq'

Everything looks fine except when I run

>abyss-fac test-unitigs.fa
abyss-fac: command not found

It seems that the only avaiable command is abyss-pe.
Any idea of what could be the problem?

Answer 1

[User 59]

If you look at the Debian package page, the only thing installed to /usr/bin is abyss-pe, which is why you can find it from the command line. Try:

/usr/lib/abyss/abyss-fac test-unitigs.fa

[Shaun Jackman]

Thanks for your response, Daniel. ABySS installs a lot of executables, 48 in fact. I installed them in /usr/lib/abyss to avoid polluting /usr/bin. I probably wouldn't do it the same way again in retrospect. Feel free to open a bug on the Debian BTS of ABySS to ask the package maintainers to move the executables to /usr/bin. I used to maintain the Debian package, but I no longer have easy access to a Debian system. I do maintain the Homebrew formula for ABySS.

[Shaun Jackman]

Ah, I remember why I installed the executables in /usr/lib/abyss. Debian requires that all executables installed in /usr/bin include a man page.

[Chip]

It worked! I didn't know this difference, thank you.