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9.7 years ago
Chip
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130
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?
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.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.It worked! I didn't know this difference, thank you.