MUMmer programs not found in path

[mthang]

Hi , I have no clue why did the installation of pymummer failed even the following programs are in the right folder. I typed "sudo pip3 install pymummer" and I keep getting this error message

nucmer -> /home/ec2-user/software/MUMmer3.23/nucmer
delta-filter -> /home/ec2-user/software/MUMmer3.23/delta-filter
show-coords -> /home/ec2-user/software/MUMmer3.23/show-coords
show-snps -> /home/ec2-user/software/MUMmer3.23/show-snps

Error message.
Complete output from command python setup.py egg_info:
Checking MUMmer programs found in path:
NOT FOUND nucmer
NOT FOUND show-coords
NOT FOUND show-snps
NOT FOUND delta-filter
Cannot install because some programs from the MUMer package not found.

[andrewjpage]

Are these programs available in your PATH? So if you type just 'nucmer' on
the command line, what happens?

On 18 July 2016 at 07:31, mthang notifications@github.com wrote:

Hi , I have no clue why did the installation of pymummer failed even the
following programs are in the right folder. I typed "sudo pip3 install
pymummer" and I keep getting this error message

nucmer -> /home/ec2-user/software/MUMmer3.23/nucmer
delta-filter -> /home/ec2-user/software/MUMmer3.23/delta-filter
show-coords -> /home/ec2-user/software/MUMmer3.23/show-coords
show-snps -> /home/ec2-user/software/MUMmer3.23/show-snps

Error message.
Complete output from command python setup.py egg_info:
Checking MUMmer programs found in path:
NOT FOUND nucmer
NOT FOUND show-coords
NOT FOUND show-snps
NOT FOUND delta-filter
Cannot install because some programs from the MUMer package not found.

—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
#21, or mute the
thread
https://github.com/notifications/unsubscribe-auth/AABeV21zYdWjRFEOt_UU1DzoWy5KrOqYks5qWx3CgaJpZM4JOcSy
.

[mthang]

Yes. They are in my PATH. When I typed "nucmer" or other commands, I can see this
USAGE: nucmer [options]
USAGE: show-snps [options]
...

I just did a temporarily fix by doing the following.

required_progs = ['/usr/local/bin/nucmer', '/usr/local/bin/show-coords', '/usr/local/bin/show-snps', '/usr/local/bin/delta-filter']

Actually, it is very odd when I typed "python setup.py install" in the pymummer folder . The error message occurs like above. However, if I just copied the "setup.py" to other location and typed "python setup.py" . I will get the following message

Checking MUMmer programs found in path:
OK nucmer
OK show-coords
OK show-snps
OK delta-filter

[andrewjpage]

Just a note to say you need to be running python3, on many systems 'python' defaults to 2.7, which is incompatible.

[ftian9]

@mthang It is because when you use sudo, the $PATH will not include /usr/local/bin.