System requirements for ErmineJ
ErmineJ should run on any platform that has Java 7 installed. If you have trouble running ErmineJ, please let us know (email@example.com).
ErmineJ is configured to use up to 1 gigabyte of RAM (1024 megabytes). If your computer does not have this much RAM installed, ErmineJ may fail to start. Under typical operating conditions, ErmineJ should not require more than ~600Mb of RAM. Memory use increases somewhat if you run multiple analyses in one session, but more dramatically if you use different sets of input genes for different analyses. This is because ErmineJ makes a partial copy of the gene annotations to match the characteristic of each set of gene scores. This is required to do correct bookkeeping of which genes are in which gene sets, without destroying the “master” annotation set, but at the cost of memory.
For example, if you are working with a generic human genome annotation set, and your gene scores only include a subset of the genes in the genome, a subsetted copy of the annotations will be created. If you perform a second analysis using a gene score file that includes a different set of genes, another copy will be made in memory.
Thus you can avoid memory problems by deleting “runs” that you are no longer interested in; and/or by limiting sessions to the analysis of a single gene score file. Memory problems that are not addressed by these measures should be reported to us (firstname.lastname@example.org)
Advanced: adjustment of memory settings
You can reduce or increase ErmineJ’s maximum memory by editing the startup script. Find the section that says “-Xmx1024m”. Change the value 1024 to be smaller or larger. Values less than 200 will almost certainly be problematic. Settings larger than ~1500 may cause problems on some computers, and in no case can you set the value to be larger than the installed RAM on the machine!