Changeset 238

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Timestamp:
07/27/09 16:02:36 (4 months ago)
Author:
cholt
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INSTALL update

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  • INSTALL

    r227 r238  
    44 
    55Note:  When using Mac OS-X and installing MAKER you must either be a system 
    6 administrator with sudo privleges or be logged in as root on the terminal for some 
    7 parts of the installation. 
     6administrator with sudo privleges or be logged in as root on the terminal for 
     7some parts of the installation. 
    88 
    99 
    …… 
    2020  a.  Download and unpack the most recent BioPerl package to a directory of your 
    2121      choice, or use Subversion to get the most current version of BioPerl. See 
    22       http://www.bioperl.org for details on how to download using Subversion. You 
    23       will then need to set PERL5LIB in your .bash_profile to the location of 
    24       bioperl (i.e. export PERL5LIB="/usr/local/bioperl-live:$PERL5LIB"). 
     22      http://www.bioperl.org for details on how to download using Subversion. 
     23      You will then need to set PERL5LIB in your .bash_profile to the location 
     24      of bioperl (i.e. export PERL5LIB="/usr/local/bioperl-live:$PERL5LIB"). 
    2525 
    2626  -full BioPerl instalation- 
    …… 
    3434  b.  Type install Bundle::CPAN on the cpan command line.  Once again just press 
    3535      enter to accept default installation options. 
    36   c.  Type install Module::Build on the cpan command line.  Once again just press 
    37       enter to accept default installation options. 
     36  c.  Type install Module::Build on the cpan command line.  Once again just 
     37      press enter to accept default installation options. 
    3838  d.  Type install Bundle::BioPerl on the cpan command line.  Once again press 
    3939      enter to accept default installation options. 
    4040  e.  Unpack the downloaded bioperl tar file to the directory of your choice or 
    4141      use Subversion to get the most up to date version.  Then use the terminal 
    42       to find the directory and type perl Build.PL in the command line, then type 
    43       ./Build test, then if all tests pass, type ./Build install.  This will 
    44       install BioPerl where perl is installed.  Press enter to accept all  
     42      to find the directory and type perl Build.PL in the command line, then 
     43      type ./Build test, then if all tests pass, type ./Build install.  This 
     44      will install BioPerl where perl is installed.  Press enter to accept all 
    4545      defaults. For Mac OS-X BioPerl will install to /Library/Perl/5.8.6/. 
    4646 
    4747 
    48483.  Install WuBlast 2.0 or higher 
    49     (WuBlast has become AB-Blast and is no longer freely available, so if you are 
    50     not lucky enough to have an existing copy of WuBlast, you can use NCBI BLAST 
    51     instead.  See NCBI BLAST documentation for installation instructions.  It is 
    52     important to note that WuBlast is a prerequisite for RepeatMasker 
    53     installation, so if you do not have WuBlast, then you will have to install 
    54     Cross_match to get RepeatMasker to work.  See RepeatMasker documentation.) 
     49    (WuBlast has become AB-Blast and is no longer freely available, so if you 
     50    are not lucky enough to have an existing copy of WuBlast, you can use NCBI 
     51    BLAST instead.  See NCBI BLAST documentation for installation instructions. 
     52    It is important to note that WuBlast is a prerequisite for RepeatMasker 
     53    installation, so if you do not have WuBlast, then you will have to install 
     54    Cross_match to get RepeatMasker to work.  See RepeatMasker documentation.) 
    5555 
    5656  a.  Unpack the tar file into the directory of your choice (i.e. /usr/local). 
    57   b.  Add the following in your .bash_profile (value depend on where you chose to 
    58       install wublast): 
     57  b.  Add the following in your .bash_profile (value depend on where you chose 
     58      to install wublast): 
    5959                export WUBLASTFILTER="/usr/local/wublast/filter" 
    6060                export WUBLASTMAT="/usr/local/wublast/matrix" 
    …… 
    65654.  Install SNAP.  Download from http://homepage.mac.com/iankorf/ 
    6666 
    67   a.  Unpack the SNAP tar file into the directory of your choice (i.e. /usr/local) 
     67  a.  Unpack the SNAP tar file into the directory of your choice (ie /usr/local) 
    6868  b.  Add the following to your .bash_profile file (value depends on where you 
    6969      choose to install snap):  export ZOE="/usr/local/snap/Zoe" 
    70   c.  Navigate to the directory where snap was unpacked (i.e. /usr/local/snap) and 
    71       type make 
     70  c.  Navigate to the directory where snap was unpacked (i.e. /usr/local/snap) 
     71      and type make 
    7272  d.  Add the location where you installed SNAP to your PATH variable in 
    7373      .bash_profile (i.e. export PATH="/usr/local/snap:$PATH"). 
    …… 
    76765.  Install RepeatMasker. Download from http://www.repeatmasker.org 
    7777 
    78   a.  The most current version of RepeatMasker requires a program called TRF. This 
    79       can be downloaded from http://tandem.bu.edu/trf/trf.html 
     78  a.  The most current version of RepeatMasker requires a program called TRF. 
     79      This can be downloaded from http://tandem.bu.edu/trf/trf.html 
    8080  b.  The TRF download will contain a single executable file.  You will need to 
    8181      rename the file from whatever it is to just 'trf' (all lower case). 
    …… 
    8383      wherever you want.  I just put it in the /RepeatMasker directory. 
    8484  d.  Unpack RepeatMasker to the directory of your choice (i.e. /usr/local). 
    85   e.  Now in the RepeatMasker directory type perl ./configure in the command line. 
    86       You will be asked to identify the location of perl, wublast, and trf.  The 
    87       script expects the paths to the folders containing the executables (because 
    88       you are pointing to a folder the path must end in a '/' character or the 
    89       configuration script throws a fit). 
     85  e.  Now in the RepeatMasker directory type perl ./configure in the command 
     86      line. You will be asked to identify the location of perl, wublast, and 
     87      trf.  The script expects the paths to the folders containing the 
     88      executables (because you are pointing to a folder the path must end in a  
     89      '/' character or the configuration script throws a fit). 
    9090  f.  Add the location where you installed RepeatMasker to your PATH variable in 
    9191      .bash_profile (i.e. export PATH="/usr/local/RepeatMasker:$PATH"). 
    92   g.  You must register at http://www.girinst.org and download the Repbase repeat 
    93       database, Repeat Masker edition, for RepeatMasker to work. 
    94   h.  Unpack the contents of the RepBase tarball into the RepeatMasker/Libraries/ 
     92  g.  You must register at http://www.girinst.org and download the Repbase 
     93      repeat database, Repeat Masker edition, for RepeatMasker to work. 
     94  h.  Unpack the contents of the RepBase tarball into the RepeatMasker/Libraries 
    9595      directory. 
    9696 
    …… 
    9999    http://www.ebi.ac.uk/~guy/exonerate 
    100100 
    101   a.  Exonerate has pre-comiled binaries for many systems; however; for Mac OS-X, 
     101  a.  Exonerate has pre-comiled binaries for many systems; however; for Mac OS-X 
    102102      you will have to download the source code and complile it yourself by 
    103103      following steps b though d. 
    104   b.  You need to have Glib and Glib 2.0 installed.  The easiest way to do this is 
    105       to install fink and then type fink install glib and fink install glib2-dev. 
     104  b.  You need to have Glib and Glib 2.0 installed.  The easiest way to do this 
     105      is to install fink and then type fink install glib and fink install 
     106      glib2-dev. 
    106107  c.  Change to the directory containing the Exonerate package to be compiled. 
    107108  d.  To install exonerate in the directory /usr/local/exonerate, type: 
    108       ./configure -prefix=/usr/local/exonerate -> then type make -> then type make 
    109       install 
     109      ./configure -prefix=/usr/local/exonerate -> then type make -> then type 
     110      make install 
    110111  e.  Add the location where you installed exonerate to your PATH variable in 
    111112      .bash_profile (i.e. export PATH="/usr/local/exonerate/bin:$PATH"). 
    …… 
    124125        export AUGUSTUS_CONFIG_PATH="where_augustus_is/config 
    125126  d.  Add the location where you installed MAKER to your PATH variable in 
    126       .bash_profile (i.e. export PATH="/usr/local/maker/bin:$PATH"). 
     127      .bash_profile (i.e. export PATH=/usr/local/maker/bin:$PATH). 
    127128  e.  You can now run a test of MAKER by following the instructions in the MAKER 
    128129      README file. 
    …… 
    139140  b.  Unpack Augustus to the directory of your choice (i.e. /usr/local). 
    140141  c.  Change to the src/ directory inside the extracted augustus folder. 
    141   d.  Install and compile Augustus by typing: make -> then type chmod +x augustus 
    142       etraining -> then type cp augustus etraining ../bin 
     142  d.  Install and compile Augustus by typing: make 
    143143  e.  Add the following to your .bash_profile file (value depends on where you 
    144       install augutus):  export AUGUSTUS_CONFIG_PATH="/usr/local/augustus/config" 
     144      install augutus):  export AUGUSTUS_CONFIG_PATH=/usr/local/augustus/config 
    145145  f.  Add the location where you installed augustus to your PATH variable in 
    146       .bash_profile (i.e. export PATH="/usr/local/augustus/bin:$PATH"). 
     146      .bash_profile (i.e. export PATH=/usr/local/augustus/bin:$PATH). 
    147147 
    148148