[Debian-med-packaging] Bug#730722: t-coffee: will become a friend of ncbi-blast+ package

[Patrice DUROUX]

Package: t-coffee
Version: 10.00.r1613-1
Severity: wishlist

Dear Maintainer,

ncbi-blast+ package is installed and regarding t_coffee default output (see bellow), it doesn't seem to
recognize it. I suspect the reason of this is that ncbi-blast+ provides /usr/bin/legacy_blast and not /usr/bin/legacy_blast.pl
Is it possible to change this default in your package or is this a trouble with ncbi-blast+ package?
(I remember discussion in Debian dev mailing list about having or not this kind of extension such 
as .pl in command name)
And finally may be t_coffee is able to suggest it then?

Regards,
Patrice



****** Multiple Sequence Alignment Methods:
--------------------------------------------
ktup_msa           built_in                                              [pg:        t_coffee is  Installed][built_in]
blastp_msa         ftp://ftp.ncbi.nih.gov/blast/executables/LATEST       [pg: legacy_blast.pl is NOT Installed][]
clustalo_msa       http://www.clustal.org/omega/                         [pg:        clustalo is  Installed][/usr/bin/clustalo]
clustalw2_msa      http://www.clustal.org                                [pg:       clustalw2 is NOT Installed][]
clustalw_msa       http://www.clustal.org                                [pg:        clustalw is  Installed][/usr/bin/clustalw]
mafftdef_msa       http://align.bmr.kyushu-u.ac.jp/mafft/online/server/  [pg:           mafft is  Installed][/usr/bin/mafft]
mafft_msa          http://align.bmr.kyushu-u.ac.jp/mafft/online/server/  [pg:           mafft is  Installed][/usr/bin/mafft]
mafftjtt_msa       http://align.bmr.kyushu-u.ac.jp/mafft/online/server/  [pg:           mafft is  Installed][/usr/bin/mafft]
mafftgins_msa      http://align.bmr.kyushu-u.ac.jp/mafft/online/server/  [pg:           mafft is  Installed][/usr/bin/mafft]
dialigntx_msa      http://dialign-tx.gobics.de/                          [pg:      dialign-tx is  Installed][/usr/bin/dialign-tx]
dialignt_msa       http://dialign-tx.gobics.de/                          [pg:       dialign-t is NOT Installed][]
poa_msa            http://www.bioinformatics.ucla.edu/poa/               [pg:             poa is  Installed][/usr/bin/poa]
probcons_msa       http://probcons.stanford.edu/                         [pg:        probcons is  Installed][/usr/bin/probcons]
probconsRNA_msa    http://probcons.stanford.edu/                         [pg:    probcons-RNA is  Installed][/usr/bin/probcons-RNA]
muscle_msa         http://www.drive5.com/muscle/                         [pg:          muscle is  Installed][/usr/bin/muscle]
mus4_msa           http://www.drive5.com/muscle/                         [pg:            mus4 is NOT Installed][]
t_coffee_msa       http://www.tcoffee.org                                [pg:        t_coffee is  Installed][/usr/bin/t_coffee]
pcma_msa           ftp://iole.swmed.edu/pub/PCMA/                        [pg:            pcma is NOT Installed][]
kalign_msa         http://msa.cgb.ki.se                                  [pg:          kalign is  Installed][/usr/bin/kalign]
amap_msa           http://bio.math.berkeley.edu/amap/                    [pg:            amap is  Installed][/usr/bin/amap]
proda_msa          http://proda.stanford.edu                             [pg:           proda is  Installed][/usr/bin/proda]
fsa_msa            http://fsa.sourceforge.net/                           [pg:             fsa is NOT Installed][]
tblastx_msa        ftp://ftp.ncbi.nih.gov/blast/executables/LATEST       [pg: legacy_blast.pl is NOT Installed][]
tblastpx_msa       ftp://ftp.ncbi.nih.gov/blast/executables/LATEST       [pg: legacy_blast.pl is NOT Installed][]
plib_msa           www.tcoffee.org                                       [pg:        t_coffee is  Installed][/usr/bin/t_coffee]


-- System Information:
Debian Release: jessie/sid
  APT prefers unstable
  APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 3.11-2-amd64 (SMP w/24 CPU cores)
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages t-coffee depends on:
ii  libc6       2.17-96
ii  libgcc1     1:4.8.2-5
ii  libstdc++6  4.8.2-5

Versions of packages t-coffee recommends:
ii  libsoap-lite-perl   0.716-1
ii  libxml-simple-perl  2.20-1
ii  tm-align            20130511+dfsg-1

Versions of packages t-coffee suggests:
ii  amap-align         2.2-4
ii  boxshade           3.3.1-8
ii  clustalw           2.1+lgpl-3
ii  dialign-tx         1.0.2-3
ii  kalign             1:2.03+20110620-2
ii  mafft              7.123-1
ii  muscle             1:3.8.31-1
ii  poa                2.0+20060928-3
ii  probcons           1.12-9
ii  proda              1.0-8
pn  seaview            <none>
pn  t-coffee-examples  <none>

-- no debconf information