root/INSTALL

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1 ***Installation Documentation***
2
3 How to Install Standard Maker
4
5 Note:  When using Mac OS-X and doing this installation you want to be logged in as
6 root on the terminal.  If you don't know how to do this, google how to enable the
7 root account on a Mac.  Type su on the command line and then type the root
8 password to log in as root once root is enabled.
9
10
11 1.  You need to have perl 5.8.0 or higher installed.  You can verify this by
12     typing perl -v on the command line in a terminal.
13
14
15 2.  Install Bioperl 1.5 or higher.  Download the Core Package from
16     http://www.bioperl.org
17
18   a.  Type perl -MCPAN -e shell into the command line to set up CPAN on your
19       computer before installing bioperl (CPAN helps install perl dependencies
20       needed to run bioperl).  For the most part just accept any default options
21       by hitting enter during setup.
22   b.  Type install Bundle::CPAN on the cpan command line.  Once again just press
23       enter to accept default installation options.
24   c.  Type install Module::Build on the cpan command line.  Once again just press
25       enter to accept default installation options.
26   d.  Type install Bundle::BioPerl on the cpan command line.  Once again press
27       enter to accept default installation options.
28   e.  Unpack the downloaded bioperl tar file to the directory of your choice.
29       Then use the terminal to find the directory and type perl Build.PL in the
30       command line, then type ./Build test, then if all tests pass type ./Build
31       install.  This will install BioPerl where perl is installed.  Press enter to
32       accept all defaults.  For Mac OS-X BioPerl will install to
33       /Library/Perl/5.8.6/ using this method.
34   f.  Alternatively you can use Subversion to keep an up to date copy of BioPerl.
35       See http://www.bioperl.org.  You will have to set PERL5LIB="path_of bioperl"
36       in your .bash_profile if you choose this method.  You must also still follow
37       steps a-d.
38
39
40 3.  Install WuBlast 2.0 or higher. (For NCBI BLAST see NCBI BLAST documentation)
41
42   a.  Unpack the tar file into the directory of your choice (i.e. /usr/local).
43   b.  Add the following in your .bash_profile (value depend on where you chose to
44       install wublast):
45                 export WUBLASTFILTER="/usr/local/wublast/filter"
46                 export WUBLASTMAT="/usr/local/wublast/matrix"
47   c.  Add the location where you installed WuBlast to your PATH variable in
48       .bash_profile (i.e. PATH="/usr/local/wublast:$PATH").
49
50
51 4.  Install SNAP.  Download from http://homepage.mac.com/iankorf/
52
53   a.  Unpack the SNAP tar file into the directory of your choice (i.e. /usr/local)
54   b.  Add the following to your .bash_profile file (value depends on where you
55       choose to install snap):  export ZOE="/usr/local/snap/Zoe"
56   c.  Navigate to the directory where snap was unpacked (i.e. /usr/local/snap) and
57       type make
58   d.  Add the location where you installed SNAP to your PATH variable in
59       .bash_profile (i.e. PATH="/usr/local/snap:$PATH").
60
61
62 5.  Install RepeatMasker. Download from http://www.repeatmasker.org
63
64   a.  The most current version of RepeatMasker requires a program called TRF. This
65       can be downloaded from http://tandem.bu.edu/trf/trf.html
66   b.  The TRF download will contain a single executable file.  You will need to
67       rename the file from whatever it is to just 'trf' (all lower case).
68   c.  Make TRF executable by typing chmod +x+u trf.  You can then move this file
69       wherever you want.  I just put it in the /RepeatMasker directory.
70   d.  Unpack RepeatMasker to the directory of your choice (i.e. /usr/local).
71   e.  Now in the RepeatMasker directory type perl ./configure in the command line.
72       You will be asked to identify the location of perl, wublast, and trf.  The
73       script expects the paths to the folders containing the executables (because
74       you are pointing to a folder the path must end in a '/' character or the
75       configuration script throws a fit).
76   f.  Add the location where you installed RepeatMasker to your PATH variable in
77       .bash_profile (i.e. PATH="/usr/local/RepeatMasker:$PATH").
78   g.  You must register at http://www.girinst.org and download the Repeat Database
79       Repeat Masker edition for RepeatMasker to work.
80   h.  Unpack the contents of the Repeat Database into the RepeatMasker/Libraries/
81       directory.
82
83
84 6.  Install Exonerate 1.4 or higher.  Download from
85     http://www.ebi.ac.uk/~guy/exonerate
86
87   a.  You will have to download the source code and complile it on your machine.
88       You will also have to install Glib.  If your using Mac OS-X you can do this
89       by typing fink install glib.
90   b.  Change to the directory containing the Exonerate package to be compiled.
91   c.  To install exonerate in the directory /usr/local/exonerate, type:
92       ./configure -prefix=/usr/local/exonerate -> then type make -> then type make
93       install
94   d.  Add the location where you installed exonerate to your PATH variable in
95       .bash_profile (i.e. PATH="/usr/local/exonerate/bin:$PATH").
96
97
98 7.  Install Augustus 2.0  Download from http://augustus.gobics.de
99
100   a.  Change to the directory containing the Augustus package to be compiled.
101   b.  Unpack Augustus to the directory of your choice (i.e. /usr/local).
102   c.  Change to the src/ directory inside the extracted augustus folder.
103   d.  Install and compile Augustus by typing: make -> tthen type chmod +x augustus
104       etraining -> then type cp augustus etraining ../bin
105   e.  Add the following to your .bash_profile file (value depends on where you
106       install augutus):  export AUGUSTUS_CONFIG_PATH="/usr/local/augustus/config"
107   f.  Add the location where you installed augustus to your PATH variable in
108       .bash_profile (i.e. PATH="/usr/local/augustus/bin:$PATH").
109
110
111 8.  Install Maker.  Download form http://www.yandell-lab.org
112
113   a.  Unpack the Maker tar file into the directory of your choice (i.e.
114       /usr/local).
115   b.  Now add the following to your .bash_profile if you haven't already:
116         export WUBLASTFILTER="where_wublast_is/filter"
117         export WUBLASTMAT="where_wublast_is/matrix"
118         export ZOE="where_snap_is/Zoe"
119         export AUGUSTUS_CONFIG_PATH="where_augustus_is/config"
120   c.  You can now run a test of Maker by following the instructions in the Maker
121       readme file.
122
123
124 See the README for instruction on installing mpi_maker
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