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

This page was last updated on Thursday, 21-Apr-2016 12:52:46 CDT

Installation notes for Jellyfish version 1.1.11 or 2.2.5

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Prerequisites

None

Version 1.x Installation

  1. $ ver="1.1.11"
  2. $ cd /programinstallers/
  3. $ wget -N http://www.cbcb.umd.edu/software/jellyfish/jellyfish-$ver.tar.gz
  4. $ tar -zxvf jellyfish-$ver.tar.gz
  5. $ cd jellyfish-$ver
  6. $ ./configure
  7. $ make
  8. $ sudo make install
    ...
    Libraries have been installed in:
       /usr/local/lib
    
    If you ever happen to want to link against installed libraries
    in a given directory, LIBDIR, you must either use libtool, and
    specify the full pathname of the library, or use the `-LLIBDIR'
    flag during linking and do at least one of the following:
       - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
         during execution
       - add LIBDIR to the `LD_RUN_PATH' environment variable
         during linking
       - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
       - have your system administrator add LIBDIR to `/etc/ld.so.conf'
    
    See any operating system documentation about shared libraries for
    more information, such as the ld(1) and ld.so(8) manual pages.
    ...
  9. Cleanup
    $ cd ..
  10. $ rm jellyfish-$ver -rf

Version 2.x Installation

  1. Rename jellyfish version 1.x (if present) to avoid overwriting. Libraries have different names so no problem there.
    $ mv /usr/local/bin/jellyfish /usr/local/bin/jellyfish1
  2. $ ver="2.2.5"
  3. $ cd /programinstallers/
  4. $ wget -N https://github.com/gmarcais/Jellyfish/releases/download/v$ver/jellyfish-$ver.tar.gz
  5. $ tar -zxvf jellyfish-$ver.tar.gz
  6. $ cd jellyfish-$ver
  7. $ ./configure
  8. $ make
  9. $ sudo make install
    ...
    Libraries have been installed in:
       /usr/local/lib
    
    If you ever happen to want to link against installed libraries
    in a given directory, LIBDIR, you must either use libtool, and
    specify the full pathname of the library, or use the `-LLIBDIR'
    flag during linking and do at least one of the following:
       - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
         during execution
       - add LIBDIR to the `LD_RUN_PATH' environment variable
         during linking
       - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
       - have your system administrator add LIBDIR to `/etc/ld.so.conf'
    
    See any operating system documentation about shared libraries for
    more information, such as the ld(1) and ld.so(8) manual pages.
    ...
  10. Test
    $ jellyfish --version
    jellyfish 2.2.5
  11. In case of this error
    jellyfish: error while loading shared libraries: libjellyfish-2.0.so.2: cannot open shared object file: No such file or directory
    add the following line to /etc/profile
    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib"
  12. Cleanup
    $ cd ..
  13. $ rm jellyfish-$ver -rf