HHPC shared software - BenLangmead/jhu-compute GitHub Wiki

We don't have root access and the cluster administrators aren't able to respond to requests to install new software, so it's pretty much up to us to install software, and we must do so as non-root users.

Please try to put software packages that others might also find useful in the shared software directory: /scratch0/langmead-fs1/shared/. I have an environment variable SHARED_DIR that points there.

Some tools installed there:

• Python (Anaconda distribution): $SHARED_DIR/anaconda
• PyPy: $SHARED_DIR/pypy-* (Portable PyPy)
• Oracle JDK 1.7: $SHARED_DIR/jdk1.7.*
• Oracle JDK 1.8: $SHARED_DIR/jdk1.8.*
• Scala: $SHARED_DIR/scala-*
• Spark: $SHARED_DIR/spark-*
• Bowtie: $SHARED_DIR/bowtie-*
• Bowtie 2: $SHARED_DIR/bowtie2-*
• SAMtools: $SHARED_DIR/samtools-*
• TopHat: $SHARED_DIR/tophat-*

Note that because we're installing as non-root users and we're all in the same langmead group, it's not possible for other users to later write to the install directory (unless we make them world read/writable). This can be a problem e.g. if one user wants to install a Python package but the Python install was made by another user.