#
# This repository no longer updated. Use akutils 1.2 instead:
# http://alk224.github.io/akutils-v1.2/
#
# **********************************************************************
# ***                                                                ***
# ***                         akutils README                         ***
# ***                                                                ***
# **********************************************************************
#
# This is a collection of scripts I wrote to make myself more productive
# while doing microbial ecology work with QIIME. I was having difficulty
# knowing that I was making the best decisions in my analyses, so I
# started writing this as an exercise in getting to know the QIIME
# commands that I was using better.  I can now use it to run many OTU
# picking workflows in a row and it generates the plots and stats that I
# like to have access to right away.  This avoids the tedium of entering
# many commands and helps to keep me organized.  For more information on
# the functionality of akutils, check out the wiki pages:
#
# https://github.com/alk224/akutils/wiki
# 
# I do everything on a Linux system (Ubuntu 14.04).  I have also tested
# most of them on CentOS 6.6 (monsoon at NAU). You should be comfortable
# installing packages and such that these scripts might require.  I will
# try to include in help functions what dependencies are required, but
# here is a short list which should cover most of these tools:
#
# 1) QIIME 1.9.0 (https://qiime.org)
# 2) ea-utils (https://code.google.com/p/ea-utils/)
# 3) Fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/)
# 4) vsearch (https://github.com/torognes/vsearch)
# 5) ITSx (http://microbiology.se/software/itsx/)
# 6) Smalt (https://www.sanger.ac.uk/resources/software/smalt/)
# 7) HMMer v3+ (http://hmmer.janelia.org/)
# 8) Mafft (http://mafft.cbrc.jp/alignment/software/)
#
# Install these and then you can use my scripts.  If they break for you,
# I probably can't help.  Mostly because I don't really have any
# computer science background and moreso because I am a graduate student
# with not a whole lot of time.  Still if you find any problems or have
# ideas for useful functionality, you can submit an issue via github:
#
# https://github.com/alk224/akutils/issues
#
# **********************************************************************
#
# Installation (two options):
#
# Install option 1: Use my new installer script (best for bare installs,
# but probably works on existing installs fine).
#
# Go to https://github.com/alk224/akutils_ubuntu_installer and follow
# the (very short) instructions.
#
# *****
#
# Install option 2: Clone the repo
# 
# You need git installed (default on many systems).
#
# git clone https://github.com/alk224/akutils.git
#
# Then add the repo directory to your path.  That should be everything,
# but to help you to know that you have everything in place, 
# dependencies and all, you should run the dependency check utility:
#
# akutils_dependency_check.sh
#
# And then check your results:
#
# akutils_dependency_check.sh result
#
# Below are
# instructions to add a directory to your path in Ubuntu or Centos as
# this sometimes confuses people.
#
# *** In Ubuntu 14.04, change /etc/environment (need sudo power). ***
#
# While anywhere, execute:
#
# sudo nano /etc/environment
#
# Add a PATH line or append your existing one.
#
# If you have to add a line, it will look like this:
#
# PATH=$PATH:/home/<userid_or_accountname>/akutils
#
# If there is already a line that looks like that, append it:
#
# PATH=$PATH:other/paths/first:/home/<userid_or_accountname>/akutils
#
# Log out and log in, reboot, or type "source /etc/environment" in
# all open terminals.
#
# *** In CentOS 6.6, modify .bashrc (should not need sudo). ***
#
# While in your home directory, execute:
#
# nano .bashrc
#
# Change PATH line as in Ubuntu instructions, then execute:
#
# export PATH
#
# Log out and log in or reboot.
#
# **********************************************************************
#
# Updating:
#
# When I make useful changes, I will push them to the repo. To benefit
# from these changes, navigate to your akutils directory and type:
#
# git pull
#
# After this, you want to rerun the config utility:
#
# akutils_config_utility.sh
#
# and choose "rebuild" to make a fresh global config file.  Older local
# config files may not function correctly after an update.  Some scripts
# may miss a variable import without a config file to match the version
# of that script.
#
# **********************************************************************
#
# Citing akutils:
#
# Andrew Krohn. (2015). akutils: Facilitating analyses of microbial 
# communities through QIIME. Zenodo. 10.5281/zenodo.18615
#