Carrot root and DNA VCRU Bioinformatics USDA ARS Vegetable Crops Research Unit

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Installation notes for MUMmer version 4.0.0beta2 Jan 23, 2018 commit 277dac5

Home Page

Prerequisites

None

Installation

  1. $ ver="3.23"
  2. $ mkdir /usr/local/bin/mummer4
  3. $ cd /programinstallers/
  4. $ git clone https://github.com/mummer4/mummer.git
  5. $ cd mummer
  6. $ autoreconf -fi
  7. $ ./configure --prefix=/usr/local/bin/mummer4
  8. $ 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
  9. $ sudo apt-get install yaggo
  10. $ ./configure --prefix=/usr/local/bin/mummer4
  11. $ 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
  12. $ nano tests/generate_sequences_cmdline.yaggo
    and replace "10M" with "10000000"
  13. $ make
  14. $ sudo make install
  15. Update the symlink
    $ cd /usr/local/bin
  16. $ rm MUMmer
  17. $ ln -s mummer4/bin MUMmer

Installation notes for MUMmer version 3.23

Home Page (3.23)

Home Page (4.x~3.9.x)

Prerequisites

Installation

  1. $ ver="3.23"
  2. $ cd /programinstallers/
  3. $ wget -N http://downloads.sourceforge.net/project/mummer/mummer/$ver/MUMmer$ver.tar.gz
  4. $ cd /usr/local/bin
  5. $ tar -zxvf /programinstallers/MUMmer$ver.tar.gz
  6. $ cd MUMmer$ver
  7. $ make check
  8. 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"
  9. $ cd -
  10. Make a version-independent symlink
    $ ln -s MUMmer$ver MUMmer
  11. $ sudo nano /etc/profile
    ...
    PATH="$PATH:/usr/local/bin/MUMmer"
    ...