INSTALL.txt

                INSTALL instructions for POTION
          (last updated 12/02/2015 - mm/dd/yyyy format)

AUTHORS
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Jorge Augusto Hongo (jorgeahongo@gmail.com)
Giovanni Marques de Castro (giomcastro@gmail.com)
Francisco Pereira Lobo (franciscolobo@gmail.com, francisco.lobo@embrapa.br)


First things first: dependencies
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A - Third-party software
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You need to install the following third-party software to use POTION:

- MUSCLE  - http://www.drive5.com/muscle/downloads.htm
- Prank   - http://wasabiapp.org/software/prank/prank_installation/
            (we recommend you to compile it yourself, instead of using the
            pre-compiled executable, see Note below)
- MAFFT   - http://mafft.cbrc.jp/alignment/software/
- PhiPack - www.maths.otago.ac.nz/~dbryant/software/PhiPack.tar
            (Phi executable)
- phylip  - http://evolution.genetics.washington.edu/phylip.html
            (seqboot, dnaml/proml and consense executables)
- PAML    - http://abacus.gene.ucl.ac.uk/software/paml.html
            (codeml executable)
- TrimAl  - http://trimal.cgenomics.org/downloads
- PhyML   - https://github.com/stephaneguindon/phyml/ 


We recommend you to download the versions for which we tested POTION's latest 
version, listed in
http://www.lmb.cnptia.embrapa.br/share/POTION/user_guide.html.

Note that you can choose between MUSCLE, Prank and MAFFT for protein multiple 
sequence alignment, and between dnaml|proml|phyml for phylogenetic tree
reconstruction, so having only one for each of these steps is enough for your
project.

To run POTION with the example datasets (MYC and TRYP), you will need Prank for
the MYC dataset, and MUSCLE for the TRYP dataset. Both will require dnaml.


Note
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Some of the programs above are compiled in C and require the library GLIBC to
run. Whenever possible, compile, them instead of using a pre-compiled binary,
as the error message "version `GLIBC_x.xx' not found" will appear in case of a
version mismatch between your computer's GLIBC and the one used to compile the
C program.

As of current writing, you can find the latest version of GLIBC in
http://www.gnu.org/software/libc/index.html



B - Perl modules
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You also need to have Perl, BioPerl, and some of its modules installed. You can
check if you have them installed in your machine with:

> perl -e 1 -M<module> 
It will return an error message if it isn't installed.

Use the commands below to check if they are installed:

perl -e 1 -MBio::SeqIO
perl -e 1 -MBio::AlignIO
perl -e 1 -MCwd
perl -e 1 -MFile::chdir
perl -e 1 -MFile::Copy
perl -e 1 -MPOSIX
perl -e 1 -MStatistics::Distributions
perl -e 1 -MStatistics::Multtest
perl -e 1 -MTie::File
perl -e 1 -MTry::Tiny
perl -e 1 -MData::Dumper
perl -e 1 -MFile::Spec::Functions
perl -e 1 -MFile::Basename
perl -e 1 -MFindBin
perl -e 1 -MCapture::Tiny
perl -e 1 -MGetopt::Long


You can install these modules through the CPAN, or manually download
(http://search.cpan.org/) and compile them. To use CPAN, you can do by 
writing:

> perl -MCPAN -e 'install "<module>"'

Use the commands below to install with CPAN:

perl -MCPAN -e 'install "Bio::SeqIO"'
perl -MCPAN -e 'install "Bio::AlignIO"'
perl -MCPAN -e 'install "Cwd"'
perl -MCPAN -e 'install "File::chdir"'
perl -MCPAN -e 'install "File::Copy"'
perl -MCPAN -e 'install "POSIX"' 
perl -MCPAN -e 'install "Statistics::Distributions"'
perl -MCPAN -e 'install "Statistics::Multtest"'
perl -MCPAN -e 'install "Tie::File"'
perl -MCPAN -e 'install "Try::Tiny"'
perl -MCPAN -e 'install "Data::Dumper"'
perl -MCPAN -e 'install "File::Spec::Functions"'
perl -MCPAN -e 'install "File::Basename"'
perl -MCPAN -e 'install "FindBin"'
perl -MCPAN -e 'install "Capture::Tiny"'
perl -MCPAN -e 'install "Getopt::Long"'



To install manually, search for the most recent version of these modules and,
for each, download and type the following (should work most of the time, except
for BioPerl):

> tar -zxvf <module.tar.gz>
> perl Makefile.PL
> make
> make test
> make install


Setting POTION environment
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Editing 'potion_config'
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Download POTION (http://www.lmb.cnptia.embrapa.br/share/POTION/downloads.html),
uncompress the .tar.gz file and place in a folder of your choice. Then edit 
POTION's configuration file (potion_config) in the 'config_files' directory. 

Write the absolute path to POTION's main directory in parameter 'potion_dir'. 
Example:

potion_dir = /home/you/programs/POTION-<version>/

This path can be found wtih the "pwd" command in your terminal. Set the absolute 
path of the third-party software IF you did not have added their path to $PATH 
variable. You can use '$potion_dir' to refer to the path in 'potion_dir'.

- codeml: path to the Codeml executable of PAML package
- consense: path to the Consense executable of Phylip package
- dnaml: path to the Dnaml executable
- mafft: path to MAFFT executable
- muscle: path to the MUSCLE executable
- phipack: path to the Phi executable of PhiPack package
- prank: path to the Prank executable
- proml: path to the Proml executable of Phylip package
- seqboot: path to the Seqboot executable of Phylip package
- trimal: path to the Trimal executable
- phyml: path to the PhyML executable