How to compile BB mapsuite with java?

Question

[sabreenaalam12345]

I have downloaded and installed the BB map suite to run stats.sh. However, the BB map suite requires compiling before running it. I have already installed java 18.0.2. for compiling, the instructions were

brew cask install java
cd jni/
JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_74.jdk/Contents/Home make -f makefile.osx
cd -
brew install --with-java open-mpi
ant -Dmpijar=/usr/local/lib/mpi.jar

To build Eclipse project with ant, you need to put ecj-4.5.2.jar to /usr/local/Cellar/ant/1.9.6/libexec/lib/.

I am not able to understand the instructions fro compiling. Can anyone tell me how should i place the commands? I have installed brew too to place out the commands.

also for running the BB mapsuite. The commands were

Running

To run with jar:

java -cp ./dist/lib/BBTools.jar align2.BBMap
java -cp ./dist/lib/BBTools.jar align2.BBMap usejni=t

How should i place the commands?

[GenoMax]

Once you download and unpack BBMap software do NOT move any files inside the folder. Simply make sure to add the directory containing BBMap software to your $PATH.

[sabreenaalam12345]

Thanks for mentioning me about the stats.sh of BBmap in my other post. I completely had no idea about this tool ever existed.

Answer 1

[ATpoint]

No, it doesn't. Follow the manual: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/installation-guide/ You can run it directly without any compilation.

[sabreenaalam12345]

The link says We can’t connect to the server at jgi.doe.gov.

[ATpoint]

That is probably due to local network/firewall issues. I tried to make some screenshots, it is really just downloading the package from SourceForge at https://sourceforge.net/projects/bbmap/ and then unpacking with tar -xvzf the_download.tar.gz. You can then run the various wrapper .sh scripts to run the BBMap utilities.

[sabreenaalam12345]

Thank you so much. I downloaded the BB tools from Sourceforge again and followed all the guidelines from the link you provided. It was able to run my fasta sequence and provided me with all the information.