Can't find show-aligns in mummer

Question

[biomagician]

Hi,

I am trying to use mummer: http://mummer.sourceforge.net/manual/#mappingdraft

to align a contig to a reference genome using:

nucmer --prefix=ref_qry ref.fasta qry.fasta

show-coords -rcl ref_qry.delta > ref_qry.coords

show-aligns ref_qry.delta refname qryname > ref_qry.aligns

show-tiling ref_qry.delta > ref_qry.tiling

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?

Thanks a lot.

C.

Answer 1

[h.mon]

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.

original answer: It seems like a bug in brew (I assume homebrew?):

TOOLS = %w[
    combineMUMs delta-filter dnadiff exact-tandems mapview mgaps
    mummer mummerplot nucmer promer repeat-match
    run-mummer1 run-mummer3 show-coords show-diff show-snps show-tiling

And then:

 TOOLS.each { |tool| bin.install_symlink prefix/tool }

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.

[biomagician]

==> Installing mummer from homebrew/science
==> Downloading https://homebrew.bintray.com/bottles-science/mummer-3.23.sierra.
Already downloaded: /Users/cr517/Library/Caches/Homebrew/mummer-3.23.sierra.bottle.3.tar.gz
==> Pouring mummer-3.23.sierra.bottle.3.tar.gz
🍺  /usr/local/Cellar/mummer/3.23: 143 files, 6.5MB

 ~ which mummer
/usr/local/bin/mummer

Does this mean mummer is installed in /usr/local/bin?

[biomagician]

Also:

3.23 pwd
/usr/local/Cellar/mummer/3.23
➜  3.23 ls
ACKNOWLEDGEMENTS     combineMUMs          nucmer2xfig
COPYRIGHT            delta-filter         promer
ChangeLog            dnadiff              repeat-match
INSTALL              docs                 run-mummer1
INSTALL_RECEIPT.json exact-tandems        run-mummer3
LICENSE              gaps                 scripts
Makefile             mapview              show-aligns
README               mgaps                show-coords
annotate             mummer               show-diff
aux_bin              mummerplot           show-snps
bin                  nucmer               show-tiling

[h.mon]

A ls -lh /usr/local/bin/mummer would confirm if mummer is indeed a symlink. If so, you could do (possibly need to be root):

ln -s /usr/local/Cellar/mummer/3.23/show-aligns /usr/local/bin/show-aligns

[biomagician]

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.