This is a test version of Biostars. For the public version, visit https://www.biostars.org.
abyss-fac: command not found on Kubuntu 14.04

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?

abyss next-gen sequencing
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updated by Ram Ram • written by Chip Chip

1 answer

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
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updated by Ram Ram • written by User 59 User 59

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

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written by Chip Chip

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.

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updated by Ram Ram • written by Shaun Jackman 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.

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updated by Ram Ram • written by Shaun Jackman Shaun Jackman

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