BBMap is a splice-aware global aligner for DNA and RNA sequencing reads. It is part of the BBTools project and includes other tools like BBDuk.
See versions of bbmap which are available:
$ module avail bbmap
Load one version into your environment and run it:
$ module load bbmap/38.67 $ bbmap.sh
Note: BBMap is multithreaded for both indexing and mapping. It will use all available threads on the host unless capped with the
t= flag. Please set this to a number that matches the number of CPUs you requested in your SLURM allocation. See the documentation for more information.
Notes from the sysadmin during installation:
$ cd /tmp/ $ wget 'https://downloads.sourceforge.net/project/bbmap/BBMap_38.67.tar.gz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fbbmap%2Ffiles%2Flatest%2Fdownload&ts=1568205639' -O BBMap_38.67.tar.gz $ tar xf BBMap_38.67.tar.gz $ sudo mkdir -p /export/apps/bbmap/38.67 $ sudo cp -r bbmap/* /export/apps/bbmap/38.67