Configure fails if ngs-sdk is not made previously

[yesimon]

Doing a clean ./configure from the source, the part configuring ngs-bam fails because it complains it cannot find ngs-sdk, which isn't made yet. So after ./configure bails, doing make -C ngs-sdk and then reconfigure and make works. It would probably be better to handle this cleanly.

CONFIGURING ngs-bam
Configuring NGS-BAM package
checking system type... Linux
checking machine architecture... x86_64
checking NGS-BAM version... 1.1.0
checking for supported architecture... x86_64 (64 bits) is supported
checking for supported OS... Linux (linux) is supported
checking for supported tool chain... gcc tool chain is supported
checking for g++... yes
checking whether gcc accepts -Wno-array-bounds... yes
checking for ngs-sdk package...
        includes... ../ngs-sdk
configure: error: required ngs-sdk package not found.

[agarwal]

I also get this error on an Ubuntu machine, but note it doesn't happen on Mac OS X. Unfortunately, I get a different error #6 on Mac, but I'm not sure there's any connection.

[kwrodarmer]

This happens for first time users, and is an issue we're aware of.

[dummey]

Can a comment linking to this ticket be added to: https://github.com/ncbi/ngs/wiki/Building-and-Installing-from-Source

[kwrodarmer]

done