From sac@neomorphic.com Wed, 12 Jan 2000 03:41:51 -0800 (PST)
Date: Wed, 12 Jan 2000 03:41:51 -0800 (PST)
From: Steve Chervitz sac@neomorphic.com
Subject: Bioperl-ANNOUNCE Re: question:bioperl remote blast error
=== This mail was sent via the Bioperl Announcement mailing list, see footer ===
James,
I've just uploaded a patch for using the run_blast_remote.pl script on
the bio.perl.org ftp site:
ftp://bio.perl.org/pub/sac/blast/Bioperl-run-blast-patch.tar.gz
or
ftp://bio.perl.org/pub/sac/blast/Bioperl-run-blast-patch.zip
This permits BLAST analysis on the NCBI server. It's not an ideal
solution, but will do for now. Check out the README in this archive
for details.
The remote BLASTing script cannot be configured to use an alternative
site, but this could be added without too much trouble. If you need
to do this now, you can edit the server URL used in the Webblast.pm
module, but any alternative site must be compatible with the NCBI web
form.
Cheers,
Steve
--
Steve A. Chervitz
sac@neomorphic.com
James Tisdall writes:
> Hi,
> using
> ./run_blast_remote.pl -prog blastx -db nr seq2.fasta
> I get an error file jimseq.blastx2.nr.temp.html with contents
>
>
> CONTENT=4;URL=http://www.ncbi.nlm.nih.gov/blast/blast.cgi>
>
> Forwarding your request to the new system
>
>
> Couldn't find a mention of this on mail list archives or docs.
> Apparently NCBI moved their service. Is there a way to configure
> bioperl to do blast remotely at ncbi or elsewhere?
>
> Many thanks,
>
> Jim
>
>
> --
> ----------------------------------------------------------------------
> James D. Tisdall Phone: (215) 728-3660
> The Fox Chase Cancer Center FAX: (215) 728-2513
> 7701 Burholme Avenue Email: JD_Tisdall@fccc.edu
> Philadelphia, Pennsylvania 19111 USA
>
Project URL: http://bio.perl.org/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl-announce.html
From sac@neomorphic.com Wed, 19 Jan 2000 10:24:37 -0800 (PST)
Date: Wed, 19 Jan 2000 10:24:37 -0800 (PST)
From: Steve Chervitz sac@neomorphic.com
Subject: Bioperl-ANNOUNCE Changing of the Guard
=== This mail was sent via the Bioperl Announcement mailing list, see footer ===
[majordomo's note: For followups see
http://www.uni-bielefeld.de/mailinglists/BCD/vsns-bcd-perl/0001/
Three cheers for Steve & Ewan ! -- Georg Fuellen]
[ Apologies if you receive multiple copies of this message.
The topic is important enough to warrant sending to all Bioperl
lists. ]
Bioperlers,
This is to announce that I am officially stepping down as chief
coordinator of the Bioperl project. I am passing the torch over to
Ewan Birney of the Sanger Center (birney@sanger.ac.uk).
Ewan has devoted a tremendous amount of energy to Bioperl over the
past year and a half and has continued to commit his resources towards
using, maintaining, enhancing the Bioperl code base.
I would like to emphasize that Bioperl is not a one-person
project. The job of the coordinator is to provide vision and to make
sure that the Bioperl distribution hangs together as an integrated
whole and generally, keeping everything is in good working order. The
writing & testing of modules, the reporting & fixing of bugs, and the
contribution of ideas & suggestions is a communal process.
Organizational & adminstrative tasks also require team effort.
I plan to remain involved with Bioperl as much as possible in
the future and I am pleased to be passing the torch to a capable
person. Take it away Ewan....
Steve Chervitz
sac@neomorphic.com
Project URL: http://bio.perl.org/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl-announce.html
From sac@neomorphic.com Wed, 12 Jan 2000 03:41:51 -0800 (PST)
Date: Wed, 12 Jan 2000 03:41:51 -0800 (PST)
From: Steve Chervitz sac@neomorphic.com
Subject: Bioperl-ANNOUNCE Re: question:bioperl remote blast error
=== This mail was sent via the Bioperl Announcement mailing list, see footer ===
James,
I've just uploaded a patch for using the run_blast_remote.pl script on
the bio.perl.org ftp site:
ftp://bio.perl.org/pub/sac/blast/Bioperl-run-blast-patch.tar.gz
or
ftp://bio.perl.org/pub/sac/blast/Bioperl-run-blast-patch.zip
This permits BLAST analysis on the NCBI server. It's not an ideal
solution, but will do for now. Check out the README in this archive
for details.
The remote BLASTing script cannot be configured to use an alternative
site, but this could be added without too much trouble. If you need
to do this now, you can edit the server URL used in the Webblast.pm
module, but any alternative site must be compatible with the NCBI web
form.
Cheers,
Steve
--
Steve A. Chervitz
sac@neomorphic.com
James Tisdall writes:
> Hi,
> using
> ./run_blast_remote.pl -prog blastx -db nr seq2.fasta
> I get an error file jimseq.blastx2.nr.temp.html with contents
>
>
> CONTENT=4;URL=http://www.ncbi.nlm.nih.gov/blast/blast.cgi>
>
> Forwarding your request to the new system
>
>
> Couldn't find a mention of this on mail list archives or docs.
> Apparently NCBI moved their service. Is there a way to configure
> bioperl to do blast remotely at ncbi or elsewhere?
>
> Many thanks,
>
> Jim
>
>
> --
> ----------------------------------------------------------------------
> James D. Tisdall Phone: (215) 728-3660
> The Fox Chase Cancer Center FAX: (215) 728-2513
> 7701 Burholme Avenue Email: JD_Tisdall@fccc.edu
> Philadelphia, Pennsylvania 19111 USA
>
Project URL: http://bio.perl.org/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl-announce.html
From sac@neomorphic.com Wed, 19 Jan 2000 10:24:37 -0800 (PST)
Date: Wed, 19 Jan 2000 10:24:37 -0800 (PST)
From: Steve Chervitz sac@neomorphic.com
Subject: Bioperl-ANNOUNCE Changing of the Guard
=== This mail was sent via the Bioperl Announcement mailing list, see footer ===
[majordomo's note: For followups see
http://www.uni-bielefeld.de/mailinglists/BCD/vsns-bcd-perl/0001/
Three cheers for Steve & Ewan ! -- Georg Fuellen]
[ Apologies if you receive multiple copies of this message.
The topic is important enough to warrant sending to all Bioperl
lists. ]
Bioperlers,
This is to announce that I am officially stepping down as chief
coordinator of the Bioperl project. I am passing the torch over to
Ewan Birney of the Sanger Center (birney@sanger.ac.uk).
Ewan has devoted a tremendous amount of energy to Bioperl over the
past year and a half and has continued to commit his resources towards
using, maintaining, enhancing the Bioperl code base.
I would like to emphasize that Bioperl is not a one-person
project. The job of the coordinator is to provide vision and to make
sure that the Bioperl distribution hangs together as an integrated
whole and generally, keeping everything is in good working order. The
writing & testing of modules, the reporting & fixing of bugs, and the
contribution of ideas & suggestions is a communal process.
Organizational & adminstrative tasks also require team effort.
I plan to remain involved with Bioperl as much as possible in
the future and I am pleased to be passing the torch to a capable
person. Take it away Ewan....
Steve Chervitz
sac@neomorphic.com
Project URL: http://bio.perl.org/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl-announce.html
From sac@neomorphic.com Wed, 12 Jan 2000 03:41:51 -0800 (PST)
Date: Wed, 12 Jan 2000 03:41:51 -0800 (PST)
From: Steve Chervitz sac@neomorphic.com
Subject: Bioperl-ANNOUNCE Re: question:bioperl remote blast error
=== This mail was sent via the Bioperl Announcement mailing list, see footer ===
James,
I've just uploaded a patch for using the run_blast_remote.pl script on
the bio.perl.org ftp site:
ftp://bio.perl.org/pub/sac/blast/Bioperl-run-blast-patch.tar.gz
or
ftp://bio.perl.org/pub/sac/blast/Bioperl-run-blast-patch.zip
This permits BLAST analysis on the NCBI server. It's not an ideal
solution, but will do for now. Check out the README in this archive
for details.
The remote BLASTing script cannot be configured to use an alternative
site, but this could be added without too much trouble. If you need
to do this now, you can edit the server URL used in the Webblast.pm
module, but any alternative site must be compatible with the NCBI web
form.
Cheers,
Steve
--
Steve A. Chervitz
sac@neomorphic.com
James Tisdall writes:
> Hi,
> using
> ./run_blast_remote.pl -prog blastx -db nr seq2.fasta
> I get an error file jimseq.blastx2.nr.temp.html with contents
>
>
> CONTENT=4;URL=http://www.ncbi.nlm.nih.gov/blast/blast.cgi>
>
> Forwarding your request to the new system
>
>
> Couldn't find a mention of this on mail list archives or docs.
> Apparently NCBI moved their service. Is there a way to configure
> bioperl to do blast remotely at ncbi or elsewhere?
>
> Many thanks,
>
> Jim
>
>
> --
> ----------------------------------------------------------------------
> James D. Tisdall Phone: (215) 728-3660
> The Fox Chase Cancer Center FAX: (215) 728-2513
> 7701 Burholme Avenue Email: JD_Tisdall@fccc.edu
> Philadelphia, Pennsylvania 19111 USA
>
Project URL: http://bio.perl.org/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl-announce.html
From sac@neomorphic.com Wed, 19 Jan 2000 10:24:37 -0800 (PST)
Date: Wed, 19 Jan 2000 10:24:37 -0800 (PST)
From: Steve Chervitz sac@neomorphic.com
Subject: Bioperl-ANNOUNCE Changing of the Guard
=== This mail was sent via the Bioperl Announcement mailing list, see footer ===
[majordomo's note: For followups see
http://www.uni-bielefeld.de/mailinglists/BCD/vsns-bcd-perl/0001/
Three cheers for Steve & Ewan ! -- Georg Fuellen]
[ Apologies if you receive multiple copies of this message.
The topic is important enough to warrant sending to all Bioperl
lists. ]
Bioperlers,
This is to announce that I am officially stepping down as chief
coordinator of the Bioperl project. I am passing the torch over to
Ewan Birney of the Sanger Center (birney@sanger.ac.uk).
Ewan has devoted a tremendous amount of energy to Bioperl over the
past year and a half and has continued to commit his resources towards
using, maintaining, enhancing the Bioperl code base.
I would like to emphasize that Bioperl is not a one-person
project. The job of the coordinator is to provide vision and to make
sure that the Bioperl distribution hangs together as an integrated
whole and generally, keeping everything is in good working order. The
writing & testing of modules, the reporting & fixing of bugs, and the
contribution of ideas & suggestions is a communal process.
Organizational & adminstrative tasks also require team effort.
I plan to remain involved with Bioperl as much as possible in
the future and I am pleased to be passing the torch to a capable
person. Take it away Ewan....
Steve Chervitz
sac@neomorphic.com
Project URL: http://bio.perl.org/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl-announce.html
From sac@neomorphic.com (Steve A. Chervitz) Wed Jan 12 11:41:51 2000
Date: Wed, 12 Jan 2000 03:41:51 -0800 (PST)
From: Steve Chervitz sac@neomorphic.com (Steve A. Chervitz)
Subject: Bioperl-ANNOUNCE Re: question:bioperl remote blast error
=== This mail was sent via the Bioperl Announcement mailing list, see footer ===
James,
I've just uploaded a patch for using the run_blast_remote.pl script on
the bio.perl.org ftp site:
ftp://bio.perl.org/pub/sac/blast/Bioperl-run-blast-patch.tar.gz
or
ftp://bio.perl.org/pub/sac/blast/Bioperl-run-blast-patch.zip
This permits BLAST analysis on the NCBI server. It's not an ideal
solution, but will do for now. Check out the README in this archive
for details.
The remote BLASTing script cannot be configured to use an alternative
site, but this could be added without too much trouble. If you need
to do this now, you can edit the server URL used in the Webblast.pm
module, but any alternative site must be compatible with the NCBI web
form.
Cheers,
Steve
--
Steve A. Chervitz
sac@neomorphic.com
James Tisdall writes:
> Hi,
> using
> ./run_blast_remote.pl -prog blastx -db nr seq2.fasta
> I get an error file jimseq.blastx2.nr.temp.html with contents
>
> <HEAD>
> <META HTTP-EQUIV=Refresh
> CONTENT=4;URL=http://www.ncbi.nlm.nih.gov/blast/blast.cgi>
> </HEAD>
> Forwarding your request to the new system
>
>
> Couldn't find a mention of this on mail list archives or docs.
> Apparently NCBI moved their service. Is there a way to configure
> bioperl to do blast remotely at ncbi or elsewhere?
>
> Many thanks,
>
> Jim
>
>
> --
> ----------------------------------------------------------------------
> James D. Tisdall Phone: (215) 728-3660
> The Fox Chase Cancer Center FAX: (215) 728-2513
> 7701 Burholme Avenue Email: JD_Tisdall@fccc.edu
> Philadelphia, Pennsylvania 19111 USA
>
Project URL: http://bio.perl.org/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl-announce.html
From sac@neomorphic.com (Steve A. Chervitz) Wed Jan 19 18:24:37 2000
Date: Wed, 19 Jan 2000 10:24:37 -0800 (PST)
From: Steve Chervitz sac@neomorphic.com (Steve A. Chervitz)
Subject: Bioperl-ANNOUNCE Changing of the Guard
=== This mail was sent via the Bioperl Announcement mailing list, see footer ===
[majordomo's note: For followups see
http://www.uni-bielefeld.de/mailinglists/BCD/vsns-bcd-perl/0001/
Three cheers for Steve & Ewan ! -- Georg Fuellen]
[ Apologies if you receive multiple copies of this message.
The topic is important enough to warrant sending to all Bioperl
lists. ]
Bioperlers,
This is to announce that I am officially stepping down as chief
coordinator of the Bioperl project. I am passing the torch over to
Ewan Birney of the Sanger Center (birney@sanger.ac.uk).
Ewan has devoted a tremendous amount of energy to Bioperl over the
past year and a half and has continued to commit his resources towards
using, maintaining, enhancing the Bioperl code base.
I would like to emphasize that Bioperl is not a one-person
project. The job of the coordinator is to provide vision and to make
sure that the Bioperl distribution hangs together as an integrated
whole and generally, keeping everything is in good working order. The
writing & testing of modules, the reporting & fixing of bugs, and the
contribution of ideas & suggestions is a communal process.
Organizational & adminstrative tasks also require team effort.
I plan to remain involved with Bioperl as much as possible in
the future and I am pleased to be passing the torch to a capable
person. Take it away Ewan....
Steve Chervitz
sac@neomorphic.com
Project URL: http://bio.perl.org/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl-announce.html
From sac@neomorphic.com (Steve A. Chervitz) Wed Jan 12 11:41:51 2000
Date: Wed, 12 Jan 2000 03:41:51 -0800 (PST)
From: Steve Chervitz sac@neomorphic.com (Steve A. Chervitz)
Subject: Bioperl-ANNOUNCE Re: question:bioperl remote blast error
=== This mail was sent via the Bioperl Announcement mailing list, see footer ===
James,
I've just uploaded a patch for using the run_blast_remote.pl script on
the bio.perl.org ftp site:
ftp://bio.perl.org/pub/sac/blast/Bioperl-run-blast-patch.tar.gz
or
ftp://bio.perl.org/pub/sac/blast/Bioperl-run-blast-patch.zip
This permits BLAST analysis on the NCBI server. It's not an ideal
solution, but will do for now. Check out the README in this archive
for details.
The remote BLASTing script cannot be configured to use an alternative
site, but this could be added without too much trouble. If you need
to do this now, you can edit the server URL used in the Webblast.pm
module, but any alternative site must be compatible with the NCBI web
form.
Cheers,
Steve
--
Steve A. Chervitz
sac@neomorphic.com
James Tisdall writes:
> Hi,
> using
> ./run_blast_remote.pl -prog blastx -db nr seq2.fasta
> I get an error file jimseq.blastx2.nr.temp.html with contents
>
> <HEAD>
> <META HTTP-EQUIV=Refresh
> CONTENT=4;URL=http://www.ncbi.nlm.nih.gov/blast/blast.cgi>
> </HEAD>
> Forwarding your request to the new system
>
>
> Couldn't find a mention of this on mail list archives or docs.
> Apparently NCBI moved their service. Is there a way to configure
> bioperl to do blast remotely at ncbi or elsewhere?
>
> Many thanks,
>
> Jim
>
>
> --
> ----------------------------------------------------------------------
> James D. Tisdall Phone: (215) 728-3660
> The Fox Chase Cancer Center FAX: (215) 728-2513
> 7701 Burholme Avenue Email: JD_Tisdall@fccc.edu
> Philadelphia, Pennsylvania 19111 USA
>
Project URL: http://bio.perl.org/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl-announce.html
From sac@neomorphic.com (Steve A. Chervitz) Wed Jan 19 18:24:37 2000
Date: Wed, 19 Jan 2000 10:24:37 -0800 (PST)
From: Steve Chervitz sac@neomorphic.com (Steve A. Chervitz)
Subject: Bioperl-ANNOUNCE Changing of the Guard
=== This mail was sent via the Bioperl Announcement mailing list, see footer ===
[majordomo's note: For followups see
http://www.uni-bielefeld.de/mailinglists/BCD/vsns-bcd-perl/0001/
Three cheers for Steve & Ewan ! -- Georg Fuellen]
[ Apologies if you receive multiple copies of this message.
The topic is important enough to warrant sending to all Bioperl
lists. ]
Bioperlers,
This is to announce that I am officially stepping down as chief
coordinator of the Bioperl project. I am passing the torch over to
Ewan Birney of the Sanger Center (birney@sanger.ac.uk).
Ewan has devoted a tremendous amount of energy to Bioperl over the
past year and a half and has continued to commit his resources towards
using, maintaining, enhancing the Bioperl code base.
I would like to emphasize that Bioperl is not a one-person
project. The job of the coordinator is to provide vision and to make
sure that the Bioperl distribution hangs together as an integrated
whole and generally, keeping everything is in good working order. The
writing & testing of modules, the reporting & fixing of bugs, and the
contribution of ideas & suggestions is a communal process.
Organizational & adminstrative tasks also require team effort.
I plan to remain involved with Bioperl as much as possible in
the future and I am pleased to be passing the torch to a capable
person. Take it away Ewan....
Steve Chervitz
sac@neomorphic.com
Project URL: http://bio.perl.org/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl-announce.html