Requirements

Last updated 2 months ago
MiGA requires a system (single computer, cluster, or cloud-computing infrastructure) with Linux or MacOS. If you simply want to access projects previously processed, all you need is ruby 1.9+ and the required gems. If you want to use MiGA to process your data, please continue these instructions.
MiGA has a relatively long list of requirements, but most of them are easy to install. Find your system below and follow the instructions for: Linux users with apt-get, MacOS users (or others with Homebrew), or any other users.
For Linux users with apt-get
Essentials
If you have apt-get, execute:
# General-purpose software
sudo apt-get install ruby ruby-sqlite3 r-base sqlite3 python
# Bioinformatics software
sudo apt-get install ncbi-blast+ hmmer bedtools \
      prodigal mcl barrnap scythe fastqc
IDBA-UD
Now install IDBA-UD (the one in apt-get is only for IDBA-Hybrid):
wget https://github.com/loneknightpy/idba/releases/download/1.1.3/idba-1.1.3.tar.gz
tar zxvf idba-1.1.3.tar.gz
cd idba-1.1.3
./configure
make
sudo install bin/idba_ud /usr/bin/
SolexaQA++
Next, you'll need to install SolexaQA++. If you have a 64-bits Linux:
curl -L -o SolexaQA++_v3.1.7.1.zip \
  "https://downloads.sourceforge.net/project/solexaqa/src/SolexaQA%2B%2B_v3.1.7.1.zip"
unzip -p SolexaQA++_v3.1.7.1.zip Linux_x64/SolexaQA++ > SolexaQA++
sudo install SolexaQA++ /usr/bin/
If you have 32-bits Linux, you can build SolexaQA++ from source:
sudo apt-get install libboost-dev libboost-filesystem-dev \
      libboost-regex-dev libboost-iostreams-dev
curl -L -o SolexaQA++_v3.1.7.1.zip \
  "https://downloads.sourceforge.net/project/solexaqa/src/SolexaQA%2B%2B_v3.1.7.1.zip"
unzip SolexaQA++_v3.1.7.1.zip 'source/*'
cd source && make
sudo install source/SolexaQA++ /usr/bin/
Ruby libraries
If you don't have direct writing privileges to the system gem repository, you can either use sudo gem ... if you have superuser access, or gem install --user ...:
gem install daemons json
R packages
This may take a while (you may need to change the last line for | sudo R --vanilla -q if your user doesn't have privileges to install R packages):
echo "
install.packages(c('enveomics.R','ape','phangorn','phytools','cluster','vegan'),
  repos='http://cran.rstudio.com/')" \
  | R --vanilla -q
MyTaxa utils
The MyTaxa utilities are optional, but without them the MyTaxa and MyTaxa scan analyses are disabled. Note that MyTaxa requires about 15Gb of disk available to store the database.
We will install the necessary software in $HOME/apps. You can change this directory if you prefer:
[[ -d $HOME/apps/bin ]] || mkdir -p $HOME/apps/bin
cd $HOME/apps
​
# Install Diamond
curl -L \
  http://github.com/bbuchfink/diamond/releases/download/v0.9.4/diamond-linux64.tar.gz \
  | tar zx
mv diamond diamond-sse2 bin/
​
# Install MyTaxa
curl -L \
  https://github.com/luo-chengwei/MyTaxa/archive/master.tar.gz | tar zx
cd MyTaxa-master
make
python utils/download_db.py
curl -O \
  http://enve-omics.ce.gatech.edu/data/public_mytaxa/AllGenomes.faa.dmnd
cd ..
​
# Install Krona
curl -L \
  https://github.com/marbl/Krona/archive/master.tar.gz | tar zx
cd bin
for i in ../Krona-master/KronaTools/scripts/*.pl ; do
  ln -sf "$i" "kt$(basename $i .pl)"
done
cd ..
For MacOS users (or others with Homebrew)
If you have MacOS, we'll use Homebrew to install most of the software. If you don't have Homebrew, execute (and follow the instructions):
/usr/bin/ruby -e "$(curl -fsSL \
      https://raw.githubusercontent.com/Homebrew/install/master/install)"
Next, make sure you have the brewsci/science and brewsci/bio taps:
brew tap brewsci/science
brew tap brewsci/bio
Essentials
Now that you have Homebrew and the science tap, execute:
# General-purpose software
brew install r sqlite3 python
brew cask install java
# Bioinformatics software
brew install blast hmmer bedtools \
      prodigal idba mcl barrnap fastqc solexaqa
brew install jonchang/biology/scythe
# Pending: Scythe in science (contacting authors)
# See: https://github.com/brewsci/homebrew-bio/issues/23
# See also: https://github.com/vsbuffalo/scythe/pull/20
Ruby libraries
If you don't have direct writing privileges to the system gem repository, you can either use sudo gem ... if you have superuser access, or gem install --user ...:
gem install sqlite3 -- \
  --with-sqlite3-lib=/usr/lib --with-sqlite3-include=/usr/include
gem install daemons json
R packages
This may take a while (you may need to change the last line for | sudo R --vanilla -q if your user doesn't have privileges to install R packages):
echo "
install.packages(c('enveomics.R','ape','phangorn','phytools','cluster','vegan'),
  repos='http://cran.rstudio.com/')" \
  | R --vanilla -q
MyTaxa utils
The MyTaxa utilities are optional, but without them the MyTaxa and MyTaxa scan analyses are disabled. Note that MyTaxa requires about 15Gb of disk available to store the database.
We will install the necessary software in $HOME/apps. You can change this directory if you prefer:
[[ -d $HOME/apps/bin ]] || mkdir -p $HOME/apps/bin
cd $HOME/apps
​
# Install Diamond (using Homebrew)
brew install diamond
​
# Install MyTaxa
curl -L \
  https://github.com/luo-chengwei/MyTaxa/archive/master.tar.gz | tar zx
cd MyTaxa-master
make
python utils/download_db.py
curl -O \
  http://enve-omics.ce.gatech.edu/data/public_mytaxa/AllGenomes.faa.dmnd
cd ..
​
# Install Krona
curl -L -o Krona.tar.gz \
  https://github.com/marbl/Krona/archive/master.tar.gz
tar zxf Krona.tar.gz
cd bin
for i in ../Krona-master/KronaTools/scripts/*.pl ; do
  ln -sf "$i" "kt$(basename $i .pl)"
done
cd ..
For any other users
Essentials
If you don't have either apt-get nor Homebrew, here's the list of requirements and URLs with installation instructions:
Ruby: https://www.ruby-lang.org/. Required version: 1.9+.
Python: https://www.python.org/.
R: http://www.r-project.org/.
SQLite3: https://www.sqlite.org/.
NCBI BLAST+: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST.
HMMer: http://hmmer.janelia.org/software. Required version: 3.0+.
Bedtools: http://bedtools.readthedocs.org/en/latest/.
Prodigal: http://prodigal.ornl.gov.
IDBA: http://i.cs.hku.hk/~alse/hkubrg/projects/idba. Required flavor:
IDBA-UD.
MCL: http://micans.org/mcl/.
Barrnap: http://www.vicbioinformatics.com/software.barrnap.shtml.
Scythe: https://github.com/vsbuffalo/scythe. Required version: 0.991+.
FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc.
SolexaQA++: http://solexaqa.sourceforge.net. Required version: v3.1.3+.
Ruby libraries
If you don't have direct writing privileges to the system gem repository, you can either use sudo gem ... if you have superuser access, or gem install --user ...:
gem install daemons json sqlite3
R packages
This may take a while (you may need to change the last line for | sudo R --vanilla -q if your user doesn't have privileges to install R packages):
echo "
install.packages(c('enveomics.R','ape','phangorn','phytools','cluster','vegan'),
  repos='http://cran.rstudio.com/')" \
  | R --vanilla -q
MyTaxa utils
The MyTaxa utilities are optional, but without them the MyTaxa and MyTaxa scan analyses are disabled. Note that MyTaxa requires about 15Gb of disk available to store the database.
To install Diamond, we provide below the method for 64-bits Linux. If you have a different system please checkout https://github.com/bbuchfink/diamond instead.
We will install the necessary software in $HOME/apps. You can change this directory if you prefer:
[[ -d $HOME/apps/bin ]] || mkdir -p $HOME/apps/bin
cd $HOME/apps
​
# Install Diamond (for 64-bits Linux)
curl -L \
  http://github.com/bbuchfink/diamond/releases/download/v0.9.4/diamond-linux64.tar.gz \
  | tar zx
mv diamond diamond-sse2 bin/
​
# Install MyTaxa
curl -L \
  https://github.com/luo-chengwei/MyTaxa/archive/master.tar.gz | tar zx
cd MyTaxa-master
make
python utils/download_db.py
curl -O \
  http://enve-omics.ce.gatech.edu/data/public_mytaxa/AllGenomes.faa.dmnd
cd ..
​
# Install Krona
curl -L \
  https://github.com/marbl/Krona/archive/master.tar.gz | tar zx
cd bin
for i in ../Krona-master/KronaTools/scripts/*.pl ; do
  ln -sf "$i" "kt$(basename $i .pl)"
done
cd ..
Part II: Getting started
Installation