annotate/README.md

ORG.Annot - Organelle Annotator

version 1.0.0 - Sept 2015

-1- Installation

First check if binaries have been already compiled for your port

scripts/check_port.sh

if it prints :

checking port compilation OK

then everything is fine

if it prints :

port not yet compiled

then, you should first compile binaries for your port please consult: src/README.txt for details

if it prints something like

XXX version A.B.C (should be >= X.Y.Z)
please consider installing XXX from src/_unix_tools_

then, you should first compile some unix tools binaries for your port please consult: src/README.txt for details

-2- Distribution organisation

• config : config file for (re)compiling tools
• data : internal data files (e.g. ChloroDB)
• detectors : features specific detector scripts
• ports : binaries for various ports
• scripts : main scripts directory
• src : sources for (re)compiling tools

-3- Usage

note: all scripts are located in scripts, so you may add this directory in your path e.g. using csh set path = ($path /scripts)

@TODO : scripts description

test

-4- Nix packages

• aragorn : Version: 1.2.38 (maintainer Bruno Bzeznik)
• clustalo
• exonerate : Version: 2.4.0 (maintainer Bruno Bzeznik)
• hmmer : Version: 3.3.2 (maintainer Markus J. Ankenbrand)
• kimono
• muscle : Version: 3.8.31 (maintainer Renato Alves)
• blast : Version: 2.11.0 (maintainer Luis Pedro Coelho)
• prokov :
• repseek
• sequtils
• sumaclust : Version: 1.0.34 (maintainer Bruno Bzeznik)
• sumatra : Version: 1.0.34 (maintainer Bruno Bzeznik)
• gawk : Version: 5.1.0
• getopt : Version: 1.1.6
• cd-hit : Version: 4.8.1 (maintainer Bruno Bzeznik)
• tcsh : Version: 6.22.03 (maintainer Anderson Torres)
• ITSx : Version: 1.1.1 (maintainer Anderson Torres)