JSOC Workflow

This repository hosts the scripts and executables for operating the JSOC pipeline workflow.

Compiling and installing

We have one executable, GetNextID, that needs to be compiled. This is done by using either CMake, for systems with Cmake >= 3.6, or by using our custom Makefile. For older machines, you may need to default to make. Both make systems allow you to install the compiled binary and copy the appropriate scripts to a runtime directory. See the following subsections for information to do this.

In general, it is good practice to remove the build and install directories if you are making changes that add or remove files in the final install directory, to make sure nothing is left over from previous builds.

CMake

If you are using CMake, the commands follow the fairly standard format. Run CMake to configure the make files, run in build mode to compile the executable, and follow in install mode to install everything needed for runtime. This is done by doing the following:

cmake -B build -D CMAKE_INSTALL_PREFIX=/some/directory/to/install/to
cmake --build build
cmake --install build

where -B build is specifying the name of the build directory ("build") which holds all the CMake information used to compile and install, -D CMAKE_INSTALL_PREFIX= is specifying the directory in which to install the executable and scripts, --build is compiling the executables, and --install is installing everything to the directory specified by CMAKE_INSTALL_PREFIX.

After running in install mode, all necessary runtime files should be in your install directory. To clear any previous CMake files, you can just delete your build directory. To remove the install directory, just delete it as well.

Makefile

If you need to use make instead, you will want to run the following commands:

make
make install MAKE_INSTALL_PREFIX=/some/directory/to/install/to

where MAKE_INSTALL_PREFIX= is specifying the directory in which to install the executable and scripts.

There is also a make uninstall target to clear out the install directory. To use this, just call make uninstall MAKE_INSTALL_PREFIX=/some/directory/to/install/to, to let it know where you installed the files. You could also just delete the install directory manually.

Modifying the repo

If you are adding new scripts or removing some, you may need to update the make systems to know which files to include in the installation. This should only be necessary if you are adding scripts that do not have the extension .csh, .pm, or .pl.