Setting path for temporary data
The Environment handling shown in figure 7.12 allows you to specify a folder for temporary data and add additional environment variables to be set when running the external application.
Figure 7.12: Temporary data should be defined for Bowtie.
In Bowtie, the post-processing step needs to access the SAM file. Thus, the working directory you set must be the directory where this SAM file will be placed, which will be in one of the directories you have configured as an Import/Export directory.
If you are running on a master-node setup, the directory you choose must be shared, that is, accessible to all nodes you plan to have as execution nodes for this task. This is because different stages of your task could be run on different nodes. For example, the export process could run on a different node than the actual execution of the Bowtie script and the post-processing. Thus, in a master-node setup, be it using grid or CLC execution nodes, having this shared temporary area eliminates the overhead of transferring the temporary files between job nodes.