Changes between Initial Version and Version 1 of PIPER


Ignore:
Timestamp:
08/18/14 11:36:20 (10 years ago)
Author:
trac
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • PIPER

    v1 v1  
     1[[PageOutline]] 
     2 
     3= Application Name = 
     4 
     5PIPE-R 
     6 
     7= Summary = 
     8 
     9* '''Name''': {{{PIPE-R}}} 
     10* '''Contact Person''': {{{Carlos Díaz, cdiaz@bsc.es}}} 
     11* '''Access Level''': {{{private}}} 
     12* '''License Agreement''': {{{GPL}}} 
     13* '''Platform''': {{{COMPSs}}} 
     14* '''Repository''': [[https://compss.bsc.es/svn/bar/apps/PIPER|PIPE-R]] 
     15 
     16 
     17== Description == 
     18A pipeline for the detection and mapping of long non-coding RNAs 
     19 
     20== Execution instructions == 
     21 
     22Change the paths in runPiper.sh to those in your machine (JAVA_HOME, etc.) and run the script from a console 
     23 
     24== Dependencies == 
     25 
     26=== T-Coffee === 
     27 
     28T-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. 
     29 
     30=== Exonerate === 
     31 
     32Exonerate 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. 
     33 
     34=== Blast === 
     35 
     36The 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. 
     37 
     38== References == 
     39 
     40* '''PIPE-R:''' https://github.com/cbcrg/piper-nf 
     41* '''T-Coffee:''' http://www.tcoffee.org/Projects/tcoffee/ 
     42* '''Exonerate:''' https://www.ebi.ac.uk/~guy/exonerate/ 
     43* '''Blast:''' http://blast.ncbi.nlm.nih.gov/ 
     44 
     45== Downloads == 
     46 
     47* '''T-Coffee:''' http://www.tcoffee.org/Packages/Stable/Latest/T-COFFEE_distribution_Version_10.00.r1613.tar.gz 
     48* '''Exonerate:''' https://www.ebi.ac.uk/~guy/exonerate/exonerate-2.2.0-x86_64.tar.gz 
     49* '''Blast:''' ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.27/ncbi-blast-2.2.27+-src.tar.gz