[[PageOutline]]

= Application Name =

PIPE-R

= Summary =

* '''Name''': {{{PIPE-R}}}
* '''Contact Person''': {{{Carlos Díaz, cdiaz@bsc.es}}}
* '''Access Level''': {{{private}}}
* '''License Agreement''': {{{GPL}}}
* '''Platform''': {{{COMPSs}}}
* '''Repository''': [[https://compss.bsc.es/svn/bar/apps/PIPER|PIPE-R]]


== Description ==
A pipeline for the detection and mapping of long non-coding RNAs

== Execution instructions ==

Change the paths in runPiper.sh to those in your machine (JAVA_HOME, etc.) and run the script from a console

== Dependencies ==

=== T-Coffee ===

T-Coffee is a multiple sequence alignment package. T-Coffee can align Protein, DNA and RNA sequences. It is also able to combine sequence information with protein structural information, profile information or RNA secondary structures.

=== Exonerate ===

Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.

=== Blast ===

The Basic Local Alignment Search Tool (BLAST) finds regions of	local similarity between sequences. The program compares nucleotide or protein	sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

== References ==

* '''PIPE-R:''' https://github.com/cbcrg/piper-nf
* '''T-Coffee:''' http://www.tcoffee.org/Projects/tcoffee/
* '''Exonerate:''' https://www.ebi.ac.uk/~guy/exonerate/
* '''Blast:''' http://blast.ncbi.nlm.nih.gov/

== Downloads ==

* '''T-Coffee:''' http://www.tcoffee.org/Packages/Stable/Latest/T-COFFEE_distribution_Version_10.00.r1613.tar.gz
* '''Exonerate:''' https://www.ebi.ac.uk/~guy/exonerate/exonerate-2.2.0-x86_64.tar.gz
* '''Blast:''' ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.27/ncbi-blast-2.2.27+-src.tar.gz