Loading a gbrowse_syn mysql database
|
View:
New views
3 Messages
—
Rating Filter:
Alert me
|
 |
Loading a gbrowse_syn mysql database
by Wes Barris
::
Rate this Message:
Hi,
The gbrowse_syn tutorial shows how to load the clustalw alignment file like this: ../bin/load_alignments_msa.pl -u root -d rice_synteny -format clustalw -v data/rice.aln However, it results in this error: wes@biodata> Generic-Genome-Browser/bin/gbrowse_syn/load_alignments_msa.pl -u root -d rice_synteny -f clustalw -v gbrowse_syn/rice/data/rice.aln Processing alignment file gbrowse_syn/rice/data/rice.aln... Processing alignment 1 Can't locate object method "num_sequences" via package "Bio::SimpleAlign" at Generic-Genome-Browser/bin/gbrowse_syn/load_alignments_msa.pl line 43, <GEN0> line 134. -- Wes Barris <wes.barris@...> ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: Loading a gbrowse_syn mysql database
by Jason Stajich-3
::
Rate this Message:
API changed in bioperl 1.6.x and beyond from no_sequences to
num_sequences so num_sequences was added then (no_sequences still works) ... You are running bioperl 1.6.x? -jason On Oct 5, 2009, at 6:19 PM, Wes Barris wrote: > Hi, > > The gbrowse_syn tutorial shows how to load the clustalw alignment > file like this: > > ../bin/load_alignments_msa.pl -u root -d rice_synteny -format > clustalw -v data/rice.aln > > However, it results in this error: > > wes@biodata> Generic-Genome-Browser/bin/gbrowse_syn/ > load_alignments_msa.pl -u root -d rice_synteny -f clustalw -v > gbrowse_syn/rice/data/rice.aln > Processing alignment file gbrowse_syn/rice/data/rice.aln... > Processing alignment 1 > Can't locate object method "num_sequences" via package > "Bio::SimpleAlign" at Generic-Genome-Browser/bin/gbrowse_syn/ > load_alignments_msa.pl line 43, <GEN0> line 134. > > -- > Wes Barris <wes.barris@...> > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry® Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart > your > developing skills, take BlackBerry mobile applications to market and > stay > ahead of the curve. Join us from November 9-12, 2009. Register > now! > http://p.sf.net/sfu/devconf > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse -- Jason Stajich jason.stajich@... jason@... ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: Loading a gbrowse_syn mysql database
by Wes Barris
::
Rate this Message:
Jason Stajich wrote:
> API changed in bioperl 1.6.x and beyond from no_sequences to > num_sequences so num_sequences was added then (no_sequences still > works) ... You are running bioperl 1.6.x? Thanks. I'm running bioperl-1.6.0. I tried updating to bioperl-live but bp_seqfeature_load.pl broke. I re-installed 1.6.0. It appears that load_alignments_msa.pl (used with gbrowse_syn) is built against bioperl-1.6.x. I just changed the load_alignments_msa.pl code to use 'no_sequences' and all is well again. > -jason > > On Oct 5, 2009, at 6:19 PM, Wes Barris wrote: > >> Hi, >> >> The gbrowse_syn tutorial shows how to load the clustalw alignment >> file like this: >> >> ../bin/load_alignments_msa.pl -u root -d rice_synteny -format >> clustalw -v data/rice.aln >> >> However, it results in this error: >> >> wes@biodata> Generic-Genome-Browser/bin/gbrowse_syn/ >> load_alignments_msa.pl -u root -d rice_synteny -f clustalw -v >> gbrowse_syn/rice/data/rice.aln >> Processing alignment file gbrowse_syn/rice/data/rice.aln... >> Processing alignment 1 >> Can't locate object method "num_sequences" via package >> "Bio::SimpleAlign" at Generic-Genome-Browser/bin/gbrowse_syn/ >> load_alignments_msa.pl line 43, <GEN0> line 134. >> >> -- >> Wes Barris <wes.barris@...> >> >> ------------------------------------------------------------------------------ >> Come build with us! The BlackBerry® Developer Conference in SF, CA >> is the only developer event you need to attend this year. Jumpstart >> your >> developing skills, take BlackBerry mobile applications to market and >> stay >> ahead of the curve. Join us from November 9-12, 2009. Register >> now! >> http://p.sf.net/sfu/devconf >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > -- > Jason Stajich > jason.stajich@... > jason@... > -- Wes Barris <wes.barris@...> ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
| Free embeddable forum powered by Nabble | Forum Help |
