Re: [Debian-med-packaging] t-coffee_5.05-1_amd64.changes REJECTED
Le Fri, Oct 05, 2007 at 02:13:20AM +0200, Steffen Moeller a écrit :
>
> You mean, M-Coffee should become a second package and modifications that
> address T-Coffee should become part of that package?
Hi Steffen, I just mean that we must make sure that t-coffee recommends the
appropriate packages and that the "-special_mode dmcoffee" works.
Unfortunately, it crashes when invoking poa on my system:
sorbet【~】$ t_coffee seqb.fasta -special_mode dmcoffee
PROGRAM: T-COFFEE (Version_5.05)
[some output cut...]
INPUT FILES
Input File (M) kalign_msa
Input File (M) t_coffee_msa
Input File (M) poa_msa
Input File (M) muscle_msa
Input File (M) mafft_msa
Input File (M) dialignt_msa
Input File (M) probcons_msa
Input File (M) amap_msa
Input File (S) seqb.fasta Format fasta_seq
INPUT SEQUENCES: 3 SEQUENCES [PROTEIN]
Input File seqb.fasta Seq Btau_1 Length 247 type PROTEIN Struct Unchecked
Input File seqb.fasta Seq Btau_2 Length 270 type PROTEIN Struct Unchecked
Input File seqb.fasta Seq Btau_3 Length 215 type PROTEIN Struct Unchecked
COMPUTE PAIRWISE SIMILARITY [dp_mode: ] [distance_matrix_mode: ktup][Similarity Measure: idmat_sim1]
Seq: Btau_1
Seq: Btau_2
Seq: Btau_3
READ/MAKE LIBRARIES:[9]
kalign_msa [method]
[Submit Job][TOT= 1][100 %][ELAPSED TIME: 0 sec.]
[Retrieve Job][TOT= 1][100 %][ELAPSED TIME: 0 sec.]
t_coffee_msa [method]
[Submit Job][TOT= 1][100 %][ELAPSED TIME: 0 sec.]
[Retrieve Job][TOT= 1][100 %][ELAPSED TIME: 0 sec.]
poa_msa [method]
[Submit Job][TOT= 1][100 %][ELAPSED TIME: 0 sec.]
Command
poa -toupper
-read_fasta /home/charles/.t_coffee/tmp/_19_7076__58_tmp4tcoffee -clustal /home/charles/.t_coffee/tmp/_19_7076__59_tmp4tcoffee /home/charles/.t_coffee/mcoffee//blosum80.mat 2>/dev/null
Failed to produce File
/home/charles/.t_coffee/tmp/_19_7076__59_tmp4tcoffee
FAILED TO EXECUTE:
poa -toupper
-read_fasta /home/charles/.t_coffee/tmp/_19_7076__58_tmp4tcoffee -clustal /home/charles/.t_coffee/tmp/_19_7076__59_tmp4tcoffee /home/charles/.t_coffee/mcoffee//blosum80.mat 2>/dev/null
# TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE]
Note to the other readers: the "d" in "dmcoffee" means "Debian"! The upstream
kindly added this variant to use only DFSG-free software :)
Have a nice day.
--
Charles Plessy
http://charles.plessy.org
Wako, Saitama, Japan
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