birdsuite install manual ubuntu 10.04 64bit

#The installation of birsuite is a little bit tricky, but finally managed to get it installed. the installation steps goes as below.

Created at 2011.11.26
Revised at
2011.12.3 |
2011.12.6 | After upgrade R to 2.14, need to reinstall the R MULUST package by doing the following
sudo R
install.packages('mclust', dep = TRUE)

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2015.09.28 Updated
I have made a docker image to run Birdsuite,
check it out at https://github.com/psytky03/Birdsuite_with_Docker
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cd ~
mkdir birdsuite
wget http://www.broadinstitute.org/ftp/pub/mpg/birdsuite/birdsuite_executables_1.5.5.tgz
tar -zxvf birdsuite_executables_1.5.5.tgz -C birdsuite


# Install Java first
sudo add-apt-repository "deb http://archive.canonical.com/ lucid partner"
sudo apt-get update
sudo apt-get install sun-java6-jre sun-java6-plugin sun-java6-fonts
java -version

#install R
sudo apt-get install r-base-core r-base-dev

# Install Numpy
sudo apt-get install python-numpy

# Install setuptools
sudo apt-get install python-setuptools

which easy_install
# the location in my case is /usr/local/bin

cd birdsuite
sudo python install.py -e /usr/local/bin/easy_install

# will get two egg files with name birdsuite-1.0-py2.5.egg and
# mpgutils-0.7-py2.5.egg in the birdsuite directory

sudo easy_install birdsuite-1.0-py2.5.egg
sudo easy_install mpgutils-0.7-py2.5.egg


#Some error message will appear like No local packages or download links found
#for birdsuite==1.0 error: Could not find suitable distribution
#for Requirement.parse('birdsuite==1.0') It is ok to ignore this.

#make the links for the two python packages installed above to the birdsuite
#folder, otherwise birsuite.sh can not find them

sudo ln -s /usr/local/bin/* .

#It is also possible to set the install directory in the birdsuite folder directly,
#check the pdf file for #python installation.

#Here start to deal with three R packages
#The broadgap.utils_1.0.tar.gz installation give some odd error message as
#Error in parse_Rd(./man/commandLineArg.Rd", encoding = "unknown", ...) :
#Figured out the error should root from the Man document in broadgap.utils_1.0.tar.gz

#Remove the Man directory and rebuild the broadgap.utils package
tar xvfz broadgap.utils_1.0.tar.gz
cd brbroadgap.utils
rm -r man
cd ..
R CMD build broadgap.utils/


R CMD INSTALL -l ~/birdsuite  broadgap.utils_1.0.tar.gz
R CMD INSTALL -l ~/birdsuite  broadgap.cnputils_1.0.tar.gz
R CMD INSTALL -l ~/birdsuite  broadgap.canary_1.0.tar.gz

# should be OK now for R

# Install the Matlab runtime

MCRInstaller.bin -console

# set the destination to ~/birdsuite/MCR75_glnx86


# I modified the run_birdseye.sh, my system is 64 bit but the run_birdsuite still recognize
# it as 32bit.

if [[ "$machine" = "x86_64" ]]
then extension=64
else extension=64
fi

#save it

#make a link of apt-probeset-summarize.64
ln -s /usr/bin/apt-probeset-summarize apt-probeset-summarize.64

#prepare the Metadatadir and others as instucted in the manual

#Finally modify the birdsuite.sh
add --exeDir=EXEDIR --metadataDir=METADATADIR to the last line

#should be ok after all this
#please do the test run using the provided data
#Do correct me if I made any mistake or let me know if there is any better ways.
#geneticsnote#gmail.com