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INSTALL
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INSTALL
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-----------------------------------------------------------
Installation
-----------------------------------------------------------
The installation procedure of structRNAfinder is done by
a shell script that have all the instructions to install the
required softwares and to download the Rfam databases.
To install type in terminal:
sudo sh install.sh
and follow the instruction.
-----------------------------------------------------------
Prompted questions
-----------------------------------------------------------
At the time of execution, the script will be asking if the user want to
install or download every particular sofware or database. The
order of the installation is the follow:
1.- Would you like to install/re-install Vienna? (y/n) [n]
If you only press enter without put a letter the answer not
(n) is taken by default.
In this part, the script downloads the source code of the Vienna
package available in:
http://www.tbi.univie.ac.at/RNA/download.php?id=viennarna-2.1.7
and compile it using the installation recommendations provided by the
authors.
2.- Would you like to install/re-install Infernal? (y/n) [n]
If you only press enter without put a letter the answer not
(n) is taken by default.
To perform this, the pre-compiled binary files are downloaded from
http://selab.janelia.org/software/infernal/infernal-1.1-linux-intel-gcc.tar.gz
extracted into a temporary folder and then copied into the Linux default
binary folder (/usr/local/bin).
3.- Would you like to download/re-download Rfam.cm? (y/n) [y]
If you only press enter without put a letter the answer yes
(y) is taken by default.
Here, the Rfam database is downloaded from
ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/Rfam.cm.gz.
Then, the necessary files to run cmscan using the cmpress program
(Infernal recomendation) are generated. By default, the path to extract
the database is the home folder of the current user. It can be changed by
the user.
4.- Would you like to install/re-install Bio::Graphics? (y/n) [y]
If you only press enter without put a letter the answer yes
(y) is taken by default.
Finally, the Perl libraries necessary to generate the images are installed.
In this part, the script install the libraries libgd-perl and Bio::Graphics
using cpan tool. If you already have it installed, or you want to install
manually, please answer “n” (not).