I have managed to do the first two commands but at the third, it tells me that 'show-aligns' is not found. 'show-tiling' is found though. I have installed mummer through brew with brew install homebrew/science/mummer. Does anybody know how I can get the show-aligns function?
edit: I opened a bug ticket an this issue has been fixed. There is now a potential conflict, because an annotation executable (also included in this fix, along with combineMUMs gaps nucmer2xfig) has been included and is also present at another package.
It seems like a bug in brew (I assume homebrew?):
So it seems a symlink to show-aligns (and some other tools) is not created. You may try to crate the symlink for yourself, but I can't help as I don't know where brew put its files and creates its symlinks.
Does this mean mummer is installed in /usr/local/bin?
ls -lh /usr/local/bin/mummerwould confirm if
mummeris indeed a symlink. If so, you could do (possibly need to be root):
Hi, Thanks, I did that and now I have show-aligns.
/usr/local/bin/mummer -> ../Cellar/mummer/3.23/bin/mummer
so /usr/local/bin/mummer is a symbolic link to ../Cellar/mummer/3.23/bin/mummer
I don't really understand symbolic links. Do you know why I have these two locations? /usr/local/Cellar/mummer... and /usr/local/bin? Why is not everything installed in the latter? I would really be grateful for a clarification.