EMBL PLugins

GBCS has been developing and maintaining several softwares (or "tools") for genomic data analysis. Most of these are command line tools, but GBCS also makes them available in the EMBL Galaxy instance .

NFS transfer tool

The NFS transfer tool is an internally developed tool that allows Galaxy users to automatically transfer the output files of their analysis to a dedicated storage location on the EMBL file server. Hence, when the user performs an analysis, two copies of intermediate and final files are created. One is stored on the file server, immediately and automatically transfered after creation thanks to the NFS transfer tool; the other copy remains in Galaxy space (as a "dataset") for further analysis.

NB. After the completion of analysis, it is advised to remove files from Galaxy space to free storage space, and keep the copy that is on the file server. 


Users defining workflows can add the tool  on each file they want to save. The above image illustrates the configuration window available in the workflow editor. The only required field is the "NFS real output directory location" where users have to indicate an absolute folder path ( /absolutepath/to/filefolder/on/filesystem/ ) where the file will be transfered . They also can indicate the filename prototype that will be used to name the transferred file. The simplest example would be where datasetname and ext are patterns (variables) that will be replaced at transfer.

The tool additionaly handles compression ( resulting in a .gzip file ) and is suitable for all types of files, including HTML reports.