Installation fixes: bump pysam and cyvcf versions and allow 'gemini update' even if initial installer fails on installing data

Aaron;
This bumps pysam and cyvcf to handle the installation issues we discussed (https://github.com/arq5x/gemini/issues/144). It also writes the gemini configuration file earlier in the process. This allows folks to do a gemini update even if the initial set of downloads failed, making redoing problematic installs easier. Now the fix is always: try a `gemini update`