Merge branch 'master' of ssh://git.metabarcoding.org/org-asm/org-annotate

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README.md

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+# ORG.Annot - Organelle Annotator
+
+**version 1.0.0 - Sept 2015**
+
+## -1- Installation
+
+# First check if binaries have been already compiled for your port
+
+```bash
+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 <ROOTDIR>/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)
+

README.txt

@@ -1,57 +0,0 @@
-#
-# ------------------------------------------
-# 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 smthing 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 <ROOTDIR>/scripts)
-#
-# @TODO : scripts description
-#
-# test