Create install script

[kelly-sovacool]

• Copy essential files + carlisle cli script to a designated directory (Create install script #93)
• Create a github action to install carlisle with this script and execute a dryrun (Test a dryrun with GitHub Actions #94)

[slsevilla]

issues

• 1. CARLISLE is not highlighted in selection Edit: there's no GUI yet
• 2. annotation dir not copied (needed for ROSE execution)
• 3. module purge is unloading ccbrpipeliner

[slsevilla]

1. CARLISLE is not highlighted after loading ccbrpipeliner
   

[slsevilla]

2. annotation dir not copied (needed for ROSE execution)

error during init, not copying annotation dir

cp: cannot stat '/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/CARLISLE/.v2.4.1-a/bin/annotation/*': No such file or directory

[slsevilla]

3. module purge is unloading ccbrpipeliner

[-] Unloading ccbrpipeliner  develop  Thank you for using ccbrpipeliner! 
Pipeline Dir: /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/CARLISLE/.v2.4.1-a/bin
fatal: not a git repository (or any parent up to mount point /gpfs)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).

[slsevilla]

4. cant find configs for tests

I don't think we outlined this, but .test dir will need to be copied too

sed: can't read /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/CARLISLE/.v2.4.1-a/bin/.test/samples.tinytest.tsv: No such file or directory
cp: cannot stat '/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/CARLISLE/.v2.4.1-a/bin/.test/contrasts.tinytest.tsv': No such file or directory

[kelly-sovacool]

@slsevilla I believe I fixed everything here except the GUI thing since we haven't made one yet.

I was able to submit a testrun to the cluster!

[slsevilla]

@kelly-sovacool - I just ran a test run and everything is working! thanks for the updates!