This is a test version of Biostars. For the public version, visit https://www.biostars.org.
mummer4: how do I get the mapview executable?

I'm following the installation manual for mummer4 on github: https://github.com/mummer4/mummer/blob/master/INSTALL.md#container-installation

I have installed the optional utilities for the plotting scripts (fig2dev,gnuplot, xfig)

I'm installing on ubuntu like this:

 wget https://github.com/mummer4/mummer/releases/download/v4.0.1/mummer-4.0.1.tar.gz
 tar -xzvf mummer-4.0.1.tar.gz
 cd mummer-4.0.1
./configure --prefix=/mummer
 make
 make check
 make install

It works fine and I can run all the "main" tools such as nucmer etc.

But I can't find an executable "mapview" as mentioned in the manual here: https://mummer.sourceforge.net/manual/#mapview

I can see a Perl script of this name, which has some placeholders for the perl version and the lib location I think, so it looks like this is supposed to be installed somewhere but I don't see an executable for it in the bin folder where all the other mummer tools were installed and the script doesn't work as-is.

What am I missing?

btw I've also followed the instructions to build a Docker container https://github.com/mummer4/mummer/blob/master/INSTALL.md#container-installation

but that also doesn't seem to create the mapview executable.

mummer mapview
• 2,953 views • link
updated by GenoMax GenoMax • written by Tospohh • Tospohh

1 answer

mapview program is deemed obsolete in v.4.x (see https://github.com/mummer4/mummer/blob/master/OBSOLETE.md ). You may need to compile it from older release (v.3.x), if you want a copy.

• 0 views • link
written by GenoMax GenoMax

oh, good catch, I didn't see that. That's a shame. The output in the examples looks very useful. Since there isn't any detail about the reason why it is obsolete. I guess I have to expect that it won't work properly with v4.x outputs. I might try v3.x. Thanks for your help!

• 0 views • link
written by Tospohh • Tospohh

As long as the output is in the right format mapview should work with v.4.x. You will need to compile it from older release.

• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this