MIKE Pipeline Makefile Help
Directory structure of a typical pipeline (assuming you choose to run mikesetup with the multiple targets makefile).
directory Reduction directory
|---makefile Makefile for multiple targets
|---target1 Directory for target1
| |----makefile Makefile for target1
|---target2 Directory for target2
|----makefile Makefile for target2
To run the MIKE Pipeline all you need to do is type "make". This will use the standard named makefile, which is name "Makefile" or "makefile".
make -f MAKEFILENAME
In order to use a non-standard named makefile type "make -f MAKEFILENAME". Non-standard named makefiles can just about be named anything.
Makefile for multiple targets
If you generated a makefile for multiple targets, the optimal choice would be to just run this makefile. This makefile is linked to the individual target makefiles. In other words when you run the multiple target makefile, it will then go and run all of the individual target makefiles. The multiple target makefile is slightly different from the individual target makefiles. It is setup such that you don't need to worry about the order things are run in, it already knows. It is probably the easiest makefile to run and also the one with the least amount of interaction.
Note: In order to have a multiple target makefile, add the following command-line argument to mikesetup; -mk MAKEFILENAME
This will remove symbolic links and re-runs mikesetup with the parameters you originally used.
This will run "make" on a specific target pipeline.
This will run "make clean" a specific target.
This will remove all of the directories and files created by mikesetup. It will not remove Final-Products directory.
Makefile for a single target
Each target generated by mikesetup has a makefile created for it. These makefiles have all stages needed to create a finished products. Some targets are depended on other targets. In other words in order to reduce the science pipelines you will need to reduce the flatfield pipelines first. Each individual pipeline has certain targets associated with them. Once reduction pipelines are finished, order doesn't matter in running the science pipeline targets.
Stage files are primarily used to determine failures in the pipeline. They are created when a particular stage has completed. In order to re-run a particular stage of the data reduction, type "make stage-STAGENAME". For this to work the particular stage file must not exist in the directory, just simply remove the file "stage-STAGENAME".
Sometimes you can just type "make" but this is under the assumption you have removed the stage file that you want to re-run and that the previous stage files exist. Otherwise make will continue to run from the last stage completed.
This will remove temporary files created by the pipeline.
This will remove all of the stage files that are created when the stage targets are completed.