Consider adding core dump to samtools about npg_conda

[kjsanger]

Location issue answered above. We only need one version of the package. The downside is only that the binaries will be a bit bigger, but we can cope with that.

[kjsanger]

Do you mean a -g build? Does that also mean htslib? There is already a Conda config file for setting CFLAGS etc (https://github.com/wtsi-npg/npg_conda/blob/devel/conda_build_config.yaml) so this is more of a build-time config question. It doesn't require changing the recipes.

[kjsanger]

If the default core dump location is a problem, we can change /proc/sys/kernel/core_pattern (execpt perhaps on RedHat if abrt is in use).

[jmtcsngr]

This came from a question from @mgcam, guess we can build with the right flags. Not sure if we want the core dumps everywhere though. Do you recommend using different versions of the package? One with core dump, one without? The htslib question is good. I guess we need both to get the whole story. The location of the dumps is a good question. Not sure how to do it. Thought by default they will dump in the pwd

[mgcam]

http://man7.org/linux/man-pages/man5/core.5.html as a reference. Looks like we need to  have unique names for these files, which is nor difficult. Changing location seems less straightforward. But might be possible where we have more control, ie 'On systems that employ systemd(1) as the init framework, core dumps may instead be placed in a location determined by systemd(1).'

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[kjsanger]

htslib, samtools and bcftools already have -g in their CFLAGS by default.