Downloading and installing

Instructions for downloading and installing Rapthor are available on the Rapthor GitLab page. Below are some recommended minimum specifications for hardware and a number of frequently asked questions regarding the installation of Rapthor.

Hardware requirements

The minimum recommended hardware is a 20-core machine with 192 GB of memory and 1 TB of disk space. Rapthor can also take advantage of multiple nodes of a compute cluster using slurm. In this mode, each node should have approximately 192 GB of memory, with a shared filesystem with 1 TB of disk space.

Installation FAQ

How can I use containers (Docker or Singularity) with Rapthor?

Containers can be used with Rapthor in two ways (see Using a (u)Docker/Singularity image for details):

  • by running it completely within the container (only for use on a single machine, no local installation of Rapthor or its dependencies is necessary)

  • by installing Rapthor locally and running only the operations (CWL workflows) within the container (for use on a single machine or on multiple nodes of a compute cluster).

A Docker image with the latest release of Rapthor and all its dependencies is available here.

How can I troubleshoot a Rapthor problem?

If you see a message in the terminal or the main log (dir_working/logs/rapthor.log) like:

CRITICAL - rapthor - Operation image_1 failed due to an error

then an error was encountered during the running of the CWL workflow of the image_1 operation. In this situation, it usually helpful to check the log files for the failed operation, which, in the case above, should be located in dir_working/logs/image_1. When Toil is used for the CWL runner (the default; see cwl_runner), filenames beginning with the word “failed” indicate the logs of the steps, if any, that failed. A search in these logs will often reveal the reason for the failure.

If the error or its cause is not clear from the log files, it may be useful to run with the debug_workflow option enabled. When this option is enabled, the working directory will never be cleaned up, stdout and stderr will not be redirectied, and the log level of the CWL runner will be set to DEBUG.