Question: abyss-fac: command not found on Kubuntu 14.04
1
gravatar for nick
4.7 years ago by
nick100
nick100 wrote:

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?

sequencing abyss next-gen • 1.6k views
ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by nick100
3
gravatar for Daniel Swan
4.7 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

If you look at the Debian package page:

https://packages.debian.org/wheezy/amd64/abyss/filelist

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
ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by Daniel Swan13k
2

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.

ADD REPLYlink written 4.7 years ago by Shaun Jackman420

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.

ADD REPLYlink written 4.7 years ago by Shaun Jackman420

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

ADD REPLYlink written 4.7 years ago by nick100
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