Re: igblast accepted - how can it be used to test igdiscover
Hi Aaron,
thanks again a lot for your helpful comments.
Am Sat, Jul 30, 2022 at 11:41:23PM -0400 schrieb Aaron M. Ucko:
> Andreas Tille <andreas@an3as.eu> writes:
>
> > into igdiscover changelog. Igblast is accepted now. However, despite I did
> > the final upload I did not checked for actual binaries which are all "hidden"
> > in usr/lib/ncbi-igblast/bin. I simply took over your and David's packaging
> > layout and cared that it builds latest upstream.
>
> Thanks for taking IgBLAST on in general. This packaging is off to a
> good start, but I'm sorry to say still not quite right. In particular:
>
> - The executables to build and install directly are igblastn and
> igblastp
I did the following attempt to seek for those binaries inside the source
tree:
diff --git a/debian/rules b/debian/rules
index fcaef90..5cf119b 100755
--- a/debian/rules
+++ b/debian/rules
@@ -21,7 +21,8 @@ override_dh_auto_build:
cd c++ && make
override_dh_auto_install:
- # skipping
+ find . -name igblastn
+ find . -name igblastp
override_dh_clean:
# cleans *.orig files, which it should not
and found the according part inside the build log:
diff --git a/debian/rules b/debian/rules
index fcaef90..5cf119b 100755
--- a/debian/rules
+++ b/debian/rules
@@ -21,7 +21,8 @@ override_dh_auto_build:
cd c++ && make
override_dh_auto_install:
- # skipping
+ find . -name igblastn
+ find . -name igblastp
override_dh_clean:
# cleans *.orig files, which it should not
I wonder what needs to be done to create the said binaries.
> along with the edit_imgt_file.pl script (which Policy 10.4
> says should be installed without its extension, though I know that's
> somewhat controversial within this team). All come from app/igblast
> and should in fact wind up in /usr/bin.
I think that controverse is over and implemented in the package
template which contains the according lintian-override[1]
> - As for other executables, supporting tools can and should come from
> ncbi-blast+ (for which I reckon a Recommends should suffice) and you
> don't need to install tests at all.
OK, pushed Recommends to Salsa (will drop superficial executables)
> - Because you're installing multiple binaries (even if fewer than at
> present), building supporting libraries dynamically should save space;
> please see ncbi-blast+ for an illustration of how to do so and
> subsequently install only those shared libraries you'll actually need
> at runtime. To avoid possible skew or missed IgBLAST-specific
> tuneups, it's probably best for the IgBLAST packaging to supply its
> own versions of these files, rather than building against libraries
> from ncbi-blast+ once a corresponding development package happens.
> (I realize that this approach goes against policy, but the libraries
> in question are at least generally native to both source bases.)
I admit that's too much for a "Team upload" done by a person who has no
idea about all the ncbi stuff.
> - Some use cases may want app/igblast's internal_data and optional_file
> subtrees, which I'd suggest installing to /usr/share/ncbi/igblast; I
> can adjust the ncbi-data package to facilitate finding those subtrees
> there.
Commited to git.
> - The package FTBFS on some architectures. Future releases should do
> better, at least on those specific fronts, but meanwhile you might
> want to copy some patches from ncbi-blast+.
I personally would simply wait for future releases. I have no interest
at all to burn my time with 32bit architectures on this package. If
someone volunteers to take over patches, I'm fine but we have lots of
open RC bugs in our packages and predepends of our packages. I consider
it not sensibly spent human resources to build this kind of packages on
hardware where it never will be used.
> Thanks again, and please let me know if you'd like further advice on any
> of those fronts. Also, sorry for not offering concrete patches; I'm
> already spread a bit too thin.
Your hints are really helpful to iteratively get things working.
Kind regards
Andreas.
[1] https://salsa.debian.org/med-team/community/package_template/-/blob/master/debian/lintian-overrides
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