spinoza is back online, it is now running CentOS 7.3 (like the new SLURM cluster), is connected to the main switch (should improve the I/O performance) and brings a whole new computing environment (more below). Big thanks to Jure from IT for setting this up!


We still have issues to solve but you are very welcome to log in and play with this new environment (please let us know if you run into issues). We would also like to mention that we are investigating ways to provide defaults so you can just type ’samtools’ and get it (more on this soon). For now, you first need to “module load a_tool” to use it.

Connection to new SLURM cluster

More help at https://wiki.embl.de/cluster/Main_Page

there are also “bsub and bjobs" tool that translates LSF bjobs/bsub instructions to SLURM equivalent.

Easybuild env available on the SLURM cluster is also available on spinoza


  • To list all available modules: module avail
  • To load a module: module load R-bundle-Bioconductor/3.3-foss-2016b-R-3.3.1
  • To unload a module: module unload R
  • To list all loaded modules in your session: module list
  • To purge all loaded modules in your session: module purge

More at easybuild.readthedocs.io

Note that you can still try to add /g/software/bin to your PATH to get the whole SEPP tool directory available ; but be aware that tools might fail to execute.



RStudio Server v1.0.136 is available at http://spinoza.embl.de. Please be aware that :

  • RStudio Studio version is different from the one running on schroedinger.
  • RStudio Server on spinoza uses the R/bioc available in easy build “R-bundle-Bioconductor/3.3-foss-2016b-R-3.3.1”. Although the R version is the same, there are few differences in some library versions; we therefore discourage you to switch back and forth between schroedinger and spinoza R Studio Server (both use your home to save your R session etc ...).
  • After few tests, we noted that .libPaths() misses the path to bioC libraries; until we understand how to fix this problem ; please update your .libPaths() the following way :
    .libPaths( c("/g/easybuild/x86_64/CentOS/7/nehalem/software/R-bundle-Bioconductor/3.3-foss-2016b-R-3.3.1", .libPaths()) )