[Debian-med-packaging] Bug#956850: Bug#956848: ncbi-blast+-legacy: Please provide /usr/bin/blastpgp.pl (including .pl extension)

Aaron M. Ucko ucko at debian.org
Mon Apr 20 15:52:40 BST 2020


Andreas Tille <tille at debian.org> writes:

> However, besides t-coffee I think that are probably more
> tools around which are expecting the .pl extensions on those prominent
> tools from ncbi-blast.

Perhaps, but please bear in mind that ncbi-blast+ primarily ships
compiled C++ binaries and blast2 historically shipped compiled C
binaries -- the scripts in question are just compatibility shims, and
ncbi-blast+-legacy uses the consolidated legacy-blast Perl script to
provide drop-in replacements for the old C binaries under their original
names, with no extensions needed.

blastpgp is one such original name, though AFAICT from a closer look at
t-coffee, the blastpgp.pl t-coffee tries to run is an EBI client script
with which I'm unfamiliar, apparently the one from its example/ subtree.

> BTW, I do not understand your third suggestion ("Better yet ...").  It
> seems you are proposing a real enhancement but I just don't get it.
> Would you mind providing a patch for t-coffee implementing this?

Sure, see below.  Please note that, per the above comment about
blastpgp.pl, this approach turned out to apply only to t-coffee's
legacy-blast(.pl) usage, which AFAICT comes solely from the
tc_generic_method.pl example, even though the C code explicitly checks
for this script's existence in some circumstances:
https://salsa.debian.org/med-team/t-coffee/-/blob/master/t_coffee_source/util_lib/aln_convertion_util.c#L5767

At any rate, legacy_blast's --print_only option helps translate command
lines like

  legacy_blast(.pl) blastpgp --path $path -d $cl_db -i $infile -o $outfile -m7 -j1

(https://salsa.debian.org/med-team/t-coffee/-/blob/master/example/tc_generic_method.pl#L2623):

  $ legacy_blast blastpgp --print_only --path \$path -d \$cl_db -i \$infile -o \$outfile -m7 -j1
  $path/psiblast -db $cl_db -query $infile -num_iterations 1 -out $outfile -outfmt 5

... where it should be safe to drop the explicit leading $path/ altogether.

I've attached a full patch.

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu

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