Re: igblast accepted - how can it be used to test igdiscover
Hi Aaron,
thanks again for your hints.
Am Mon, Aug 01, 2022 at 12:14:32PM -0400 schrieb Aaron M. Ucko:
> > I wonder what needs to be done to create the said binaries.
>
> Ah, right, they need VDB; please try adding a build dependency on
> libncbi-vdb-dev and removing --without-vdb from the configure command
> line.
I've done so[1] but it does not really help. The `find . ` statements
do not create any result. I've now bumped the execution time for the
build in Salsa CI to have some result for future pushs - so you can not
see yet the full build log.
Do you have any other hint how to create the main binaries reliably?
General question @Steffen: You added a lot of `--without-*` options
which are not really clear to me. Some might be motivated by missing
support in Debian but openmp, protobuf and others are supported in
Debian (not to speak about Pythono and Perl).
> Also, you can perform a more targeted build by adding
> --with-flat-makefile and then changing the build command to
>
> cd c++/*/build && make -f Makefile.flat app/igblast/
>
> where the trailing slash is mandatory. (This approach will still yield
> some ancillary binaries, namely internal builds tools.)
I missed to push this but have this in my local repository now.
> > I admit that's too much for a "Team upload" done by a person who has no
> > idea about all the ncbi stuff.
>
> That's fair; you can leave the build static for now and I'll take care of
> those adjustments when I get a chance. Likewise for portability issues,
> though as noted you probably won't have to look far for patches.
Thanks a lot.
Kind regards
Andreas.
[1] https://salsa.debian.org/med-team/ncbi-igblast/-/commit/c70ea988bf68ca4bfe761244cb585a8c27c671fe
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