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
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