The purpose of this test is to verify that the newest version of the hdf5-library can still
be used by pac-bioload.

This test uses the newest Fedora distribution ( it has the newest version of the hdf5-library
included in its package manager ) as well as docker to perform the test.

You need:
1) docker installed on your machine
2) docker to be configured to be usable by your user-account
3) internet access to github and docker-hub
4) a valid HDF5-submission from a Pacbio machine accessible from your machine

Before you can run the script "test_using_docker_and_hdf5_submission.sh", edit this script.
You have to edit lines 22, 38, and 40.

In line 22 you have to replace "VDB-5712" with "engineering" in case the branch VDB-5712
does not exist any more on github.

In line 38 you have to replace "/mnt/data/SRA/ACC/PACBIO/HDF5_SRC" with the location of
your Pacbio submission.

In line 40 you have to replace "m130621_024744_42150_c100527702550000001823082709281355_s1_p0.1.bax.h5"
with the filename of a valid Pacbio submission.

Most Pacbio-submissions come in the form of multiple files. There is a small "package descriptor"
file that lists the actual data files. If you use this smaller one, all of the data files will be
loaded, which will take longer. For a shorter test, use just one of the data files.

The script will create a docker-image based on Fedora-latest. It will install all neccessary
development tools, 3rd-party libraries, and the source-code of the SRA-toolkit from docker-hub,
github, and the fedora-repository. After that it will compile the whole SRA-toolkit.
This is tested for Fedora-latest in September 2024. It may be neccessary to adjust package names
in the future in case building of the image fails. At the end it will start a docker-container
and let it run pacbio-load on the Pacbio submission you provided in lines 38 and 40 of the script.
The load should end with a success message. The script removes the docker-container after use
but not the image. You might want to remove the image manually since it is large.
