TIL: When Picard tools spill to disk, they write temporary files to the system's default temporary directory, which is typically tmp on Linux systems. However, you can control where Picard writes temporary files by specifying the `TMP_DIR` option. For example:
If you are running Picard on a system with limited space in tmp, it is a good idea to set `TMP_DIR` to a directory with sufficient space, such as a scratch directory (`$WORKSPACE` in your case).
TIL: You can get a list of Spark-enabled GATK tools with the command
gatk --list | grep Spark
(The website doesn't seem to have a list anywhere)
Anyone have advice on how to get the Spades genome assembler to use less memory?
Published version of CAGEE!
Here, we present a new software package (Computational Analysis of Gene Expression Evolution [CAGEE]) for inferring patterns of increases and decreases in gene expression across a phylogenetic tree, as well as the rate at which these changes occur. CAGEE can calculate genome-wide rates of gene expression, along with ancestral states for each gene.
#phylogenetics #bioinformatics
Just compiling up a version of NCBI Blast for use on a large node. Anyone know why it looks for Boost/LaPack/GSL but doesn't require them? Will it be faster if I make them available?