Agalma installation scripts

ubuntu_amazon_tarball.sh

# This is a full set of commands to install [Agalma](https://bitbucket.org/caseywdunn/agalma) 
# from the on Ubuntu Server from the tarballs. It has been tested on the AWS Ubuntu Server AMI.
# 

sudo apt-get update
sudo apt-get install make

wget https://bitbucket.org/caseywdunn/biolite/raw/master/install_biolite_ubuntu.sh
sudo sh install_biolite_ubuntu.sh
wget https://bitbucket.org/caseywdunn/agalma/raw/master/install_agalma_ubuntu.sh
sudo sh install_agalma_ubuntu.sh
sudo agalma blastdb

export BIOLITE_RESOURCES="threads=4,memory=7G" # Amazon c3.xlarge

mkdir ~/tmp
cd ~/tmp
agalma test

ubuntu_desktop_git.sh

# This is a full set of commands to install [Agalma](https://bitbucket.org/caseywdunn/agalma) 
# from the git repository on Ubuntu Desktop. As written, it installs from the devel branch (ie, 
# NOT a release).
# 
# versions tested:
# Ubuntu 13.10 (fully updated on March 15, 2014)
# BioLite commit d649d228242701ffa981bdb30133b30e56bb854f (had to cherypick build_3rd_party.sh from master to pick up a hitfix)
# Agalma  commit 29acedbe8ae6daf38f733ca259a839002867ff8b
 

# Basics
sudo apt-get update
sudo apt-get install -y git

mkdir ~/src
cd ~/src

# Biolite
git clone https://caseywdunn@bitbucket.org/caseywdunn/biolite.git
cd biolite
git checkout devel
git pull
sudo sh install_biolite_ubuntu.sh
cd ..


# Agalma
git clone https://caseywdunn@bitbucket.org/caseywdunn/agalma.git
cd agalma
git checkout devel
git pull
sudo sh install_agalma_ubuntu.sh
sudo agalma blastdb

# Run the test
export BIOLITE_RESOURCES="threads=2,memory=4G"
mkdir ~/tmp
cd ~/tmp
agalma test

# Run the tutorial
cd ~/src/agalma
grep '^    ' TUTORIAL.md | sed -e 's/^    //' > tutorial.sh
bash tutorial.sh

# Developing code
# If you edit the source and would like to try it out, you don't have to redo all this. You just need the following two lines:
# ./autogen.sh
# sudo make install

ubuntu_git_agalma_0.4.sh

# Basics
sudo apt-get update
sudo apt-get install -y python-pip

# install bib
sudo apt-get install -y build-essential gcc-4.4 g++-4.4 cmake curl git unzip default-jre-headless libncurses5-dev zlib1g-dev
bash -c "$(curl -fsSL https://bitbucket.org/mhowison/bib/raw/master/install.sh)"
echo "export PATH=/opt/bib/active/bin:\$PATH" >>~/.bash_profile
source ~/.bash_profile

# install biolite
sudo apt-get install -y python-dev # Required for biopython installation
sudo apt-get install -y libxml2-dev libxslt1-dev # Required for lxml
sudo pip install biopython dendropy docutils networkx numpy lxml wget
sudo apt-get install -y python-matplotlib # installing via pip does not include freetype etc

mkdir ~/src
cd ~/src # Avoid collission between agalma source directory and agalma analysis directory from tutorial

git clone https://bitbucket.org/caseywdunn/biolite.git
cd biolite
git fetch
git checkout release-0.4.0
sudo python setup.py install # install fails without sudo

# install agalma
sudo apt-get install -y libfindbin-libs-perl # Required for transdecoder
sudo cpan -i URI::Escape # Required for transdecoder
bib install -f biolite-tools/0.4.0 blast/2.2.29+ bowtie/1.0.0 bowtie2/2.1.0 fastqc/0.10.1 gblocks/0.91b jellyfish/1.1.11 mafft/7.130 mcl/12-135 parallel/20130922 raxml/7.7.6 rsem/1.2.9 samtools/0.1.19 sratoolkit/0.2.3.4-2 transdecoder/r2012-08-15 trinity/r2013_08_14
cd ~/src
git clone https://bitbucket.org/caseywdunn/agalma.git
cd agalma
git fetch
git checkout release-0.4.0
sudo python setup.py install

# test
mkdir ~/tmp
cd ~/tmp # test polutes working directory, provide a space for the test
agalma test

# Tutorial
cd ~/src/agalma
grep '^    ' TUTORIAL.md | sed -e 's/^    //' > tutorial.sh
cd ~/
bash src/agalma/tutorial.sh &> tutorial.log

On a minimal install (EC2 AMI), I also had to install these for pip to build lxml:

sudo apt-get install -y libxml2-dev libxslt1-dev

Then transdecoder broke and needed these perl modules:

sudo apt-get install -y libfindbin-libs-perl
sudo cpan -i URI::Escape 

Thanks Mark - just folded these in.