This page was last updated on Monday, 02-Dec-2019 16:37:02 CST
Installation notes for MUMmer version 4.0.0beta2 Jan 23, 2018 commit 277dac5
Home Page
Prerequisites
None
- g++
- csh
$ sudo apt-get install csh
Installation
- $ ver="3.23"
- $ mkdir /usr/local/bin/mummer4
- $ cd /programinstallers/
- $ git clone https://github.com/mummer4/mummer.git
- $ cd mummer
- $ autoreconf -fi
- $ ./configure --prefix=/usr/local/bin/mummer4
- $ make
YAGGO src/umd/nucmer_cmdline.hpp
Makefile:2791: recipe for target 'src/umd/nucmer_cmdline.hpp' failed
make: *** [src/umd/nucmer_cmdline.hpp] Error 1
- $ sudo apt-get install yaggo
- $ ./configure --prefix=/usr/local/bin/mummer4
- $ make
on carrot and daucus servers only:
YAGGO src/umd/nucmer_cmdline.hpp
YAGGO tests/generate_sequences_cmdline.hpp
tests/generate_sequences_cmdline.yaggo:17: In Option genome-size|G: Option genome-size|G: Invalid unsigned integer '10M'
Makefile:2791: recipe for target 'tests/generate_sequences_cmdline.hpp' failed
make: *** [tests/generate_sequences_cmdline.hpp] Error 1
- $ nano tests/generate_sequences_cmdline.yaggo
and replace "10M" with "10000000"
- $ make
- $ sudo make install
- Update the symlink
$ cd /usr/local/bin
- $ rm MUMmer
$ ln -s mummer4/bin MUMmer
Installation notes for MUMmer version 3.23
Home Page (3.23)
Home Page (4.x~3.9.x)
Prerequisites
- g++
- csh
$ sudo apt-get install csh
Installation
- $ ver="3.23"
- $ cd /programinstallers/
- $ wget -N http://downloads.sourceforge.net/project/mummer/mummer/$ver/MUMmer$ver.tar.gz
- $ cd /usr/local/bin
- $ tar -zxvf /programinstallers/MUMmer$ver.tar.gz
- $ cd MUMmer$ver
- $ make check
- from
http://sourceforge.net/p/mummer/discussion/451664/thread/59ad55aa/ we learn that
there is a flag needed to handle larger genomes
A sample error message where this happens: ERROR: mummer and/or mgaps returned non-zero
$ make CPPFLAGS="-O3 -DSIXTYFOURBITS"
- $ cd -
- Make a version-independent symlink
$ ln -s MUMmer$ver MUMmer
- $ sudo nano /etc/profile
...
PATH="$PATH:/usr/local/bin/MUMmer"
...