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

[Olivier Sallou]

On 11/28/2013 06:26 PM, Patrice DUROUX wrote:
> 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?
Hi,
as co-maintainter  of ncbi-blast+ package, I'd like to point the fact
that, indeed, Debian rules asks to remove extensions in bin directory.
This is why ncbi legacy package removed .pl extensions on binaries.

This extension management is sometimes a problem for packages
interoperability....but rules are rules  :-)

Olivier
> (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
>
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-- 
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95

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