getfastq and prefetch 2.8.0. about amalgkit HOT 5 CLOSED

ah, found out that it was a different bug that caused prefetch to fail, which will be fixed with the next push.

prefetch 2.8. still complains about --output-directory not existing, but just ignores it.

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short update:
even though the download finishes successfully in prefetch 2.8., amalgkit will throw an error afterwards, because it can't find the .sra in the working directory.
prefetch 2.8. downloads sra data into /ncbi/public/sra/ unless the user changed the sratoolkit config itself.

I fixed both the parameter error and added a check for /ncbi/public/sra/ as well. So both legacy and stable prefetch versions are supported.

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We should let amalgkit automatically changes its behavior depending on the prefetch versions. Cou.d you work on this? I'll push one commit today so please update your local later.

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Pushed. Done faster than I thought. Also, we've started managing the amalgkit version in init.py. Please update it when you push.

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gotcha!

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