Cluster notes

An incomplete list of the clusters cmuts has been built and run on. Since cmuts plot requires a browser to view the report, it should be run locally.

Stanford Sherlock

Pre-Built

Only cmuts align has dependencies. minimap2 and samtools are loaded as modules:

ml load biology minimap2/2.30 samtools/1.16.1

For paired-end data, vsearch must be installed separately; see the download instructions. Sherlock needs the Linux x86_64 build whose name ends in -ubi7.

Source Builds

The cmuts align dependencies listed above are unchanged. Running also needs HDF5 and htslib, the latter provided by the samtools module:

ml load hdf5/1.12.0
ml load biology samtools/1.16.1

In addition, building needs a later GCC:

ml load gcc/12.4.0

HHMI Janelia

Running needs htslib on the path and its libraries alongside:

ml load samtools
export LD_LIBRARY_PATH=/misc/local/samtools-1.22.1/lib:$LD_LIBRARY_PATH

Building needs htslib where pkg-config will find it:

export PKG_CONFIG_PATH=/misc/local/samtools-1.22.1/lib/pkgconfig:$PKG_CONFIG_PATH