a couple of problems on CentOS 8 #12
Description
There are a couple of small issues when building ngs-sdk on CentOS 8.
(1) In $TOPDIR/share/examples-java/Makefile NGS_CLASS_PATH is defined but the javac line is:
javac $(DEBUGGING) $^ -d .
when it needs to be:
javac -classpath $(NGS_CLASS_PATH) $(DEBUGGING) $^ -d .
This may be related to (5), below, as there was no CLASSPATH defined in the environment.
(2) In the source directories ngs-python/Makefile.python refers to "python", but there is no such beast on RH derivatives, only python2 or python3. The file was modified to use "python3".
(3) On the system in question the python packages are installed into /usr/common/lib/python3.6/site-packages (which is NFS shared with other machines) by setting PYTHONPATH to that value. The supplied Makefile in that directory ignored PYTHONPATH, so installation was done manually by:
cd /usr/common/src/ncbi/ngs/ngs-python
python3 setup.py install --prefix=/usr/common 2>&1 \
| tee ../install_python_2020_05_11.log
The default installation of the ngs python pieces goes into "~/.local".
(4) The build leaves a large directory ~/ncbi-outdir even after installation.
This directory is not discussed at all in the installation instructions:
https://github.com/ncbi/ngs/wiki/Building-and-Installing-from-Source
This should be documented, especially a comment about when it is safe to remove it.
(5) The installation instructions end with:
At this point, the installation should be complete, although you will probably have to login again before all changes take place. If the installation is successful, you should find library code installed and an update to shell variables (only AFTER logging in again). To verify update of your environment:
$ echo $LD_LIBRARY_PATH # should now have the path to your installed ngs libraries
$ echo $CLASSPATH # should now have the path to your installed ngs jar
I do not see any modifications to login configuration files (nor would I want the installation to do that automatically.) In a newly logged in session, after installation, neither LD_LIBRARY_PATH nor CLASSPATH were set as indicated. If this was supposed to happen with one of the "make install" steps, that must have failed.