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

This page was last updated on Saturday, 19-Nov-2016 15:54:00 CST

Installation notes for bfast version 0.7.0a

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Prerequisites

Installation

  1. $ ver=""
  2. $ cd /programinstallers/
  3. $ git clone git://bfast.git.sourceforge.net/gitroot/bfast/bfast
  4. $ cd bfast
  5. $ sh autogen.sh
  6. $ ./configure
  7. $ make
  8. Ubuntu 16.04 two header files had inline functions declared that did not match code in .c file, remove "inline" from
    inline char ToUpper(char);
    in bfast/BLib.h
    and twice from
    inline int32_t ScoringMatrixGetNTScore(char, char, ScoringMatrix*);
    inline int32_t ScoringMatrixGetColorScore(char, char, ScoringMatrix*);

    in bfast/ScoringMatrix.h
  9. $ make install
  10. Error installing docs
    test -z "/usr/local/share/doc/bfast" || /bin/mkdir -p "/usr/local/share/doc/bfast"
    /bin/mkdir: cannot create directory `/usr/local/share/doc': Permission denied

    so do this
    $ sudo mkdir /usr/local/share/doc && sudo chmod 777 /usr/local/share/doc
  11. 4
  12. Copy the utility programs too
    $ cp -pu /programinstallers/bfast/butil/btestindexes /usr/local/bin/
    There are some other utilities I did not copy