Re: [Bioperl-l] Next-gen modules

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	Re: [Bioperl-l] Next-gen modules by Cook, Malcolm-2 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Some parts of this message have been removed. Learn more about Nabble's security policy. Lincoln? Scot? Hi there! How do I get the permissions I need if Lincoln wants me to submit the patch below which fixes this bug: http://rt.cpan.org/Public/Bug/Display.html?id=50532 % cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co gbrowse-adaptors/Bio-SamTools Cheers, --Malcolm Cook - Stowers Institute for Medical Research * Sam.pm.~1.18.~ Thu Sep 24 14:57:53 2009 --- Sam.pm Fri Oct 23 11:05:14 2009 *********** * 1219,1230 **** my $expand_flags = $args{-expand_flags}; my $split_splices = $args{-split} \|\| $args{-split_splices}; ! -e $bam_path && -r _ or croak "$fa_path does not exist or is not readable"; my $bam = Bio::DB::Bam->open($bam_path) or croak "$bam_path open: $!"; my $fai; if ($fa_path) { ! -e $fa_path && -r _ or croak "$fa_path does not exist or is not readable"; $fai = Bio::DB::Sam::Fai->open($fa_path) or croak "$fa_path open: $!"; } --- 1219,1232 ---- my $expand_flags = $args{-expand_flags}; my $split_splices = $args{-split} \|\| $args{-split_splices}; ! -e $bam_path or croak "$bam_path does not exist"; ! -r _ or croak "is not readable"; my $bam = Bio::DB::Bam->open($bam_path) or croak "$bam_path open: $!"; my $fai; if ($fa_path) { ! -e $fa_path or croak "$fa_path does not exist"; ! -r _ or croak "$fa_path is not readable"; $fai = Bio::DB::Sam::Fai->open($fa_path) or croak "$fa_path open: $!"; } ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) 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/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
	Re: [Bioperl-l] Next-gen modules by Scott Cain-4 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Hi Malcolm, You need a SourceForge user account that you'll tell me, so I can give you developer permissions, and then get an svn checkout of the gbrowse-adaptors repo (we switched to svn last month). Scott On Fri, Oct 23, 2009 at 12:16 PM, Cook, Malcolm <MEC@...> wrote: > Lincoln? Scot? > > Hi there! > > How do I get the permissions I need if Lincoln wants me to submit the patch > below which fixes this bug: > http://rt.cpan.org/Public/Bug/Display.html?id=50532 > > % cvs -d :pserver:anonymous@...:/cvsroot/gmod co > gbrowse-adaptors/Bio-SamTools > > Cheers, > > --Malcolm Cook - Stowers Institute for Medical Research > > > > * Sam.pm.~1.18.~ Thu Sep 24 14:57:53 2009 > --- Sam.pm Fri Oct 23 11:05:14 2009 > *********** > * 1219,1230 **** > my $expand_flags = $args{-expand_flags}; > my $split_splices = $args{-split} \|\| $args{-split_splices}; > > ! -e $bam_path && -r _ or croak "$fa_path does not exist or is not > readable"; > my $bam = Bio::DB::Bam->open($bam_path) or croak "$bam_path open: > $!"; > > my $fai; > if ($fa_path) { > ! -e $fa_path && -r _ or croak "$fa_path does not exist or is not > readable"; > $fai = Bio::DB::Sam::Fai->open($fa_path) or croak "$fa_path open: > $!"; > } > > --- 1219,1232 ---- > my $expand_flags = $args{-expand_flags}; > my $split_splices = $args{-split} \|\| $args{-split_splices}; > > ! -e $bam_path or croak "$bam_path does not exist"; > ! -r _ or croak "is not readable"; > my $bam = Bio::DB::Bam->open($bam_path) or croak "$bam_path open: > $!"; > > my $fai; > if ($fa_path) { > ! -e $fa_path or croak "$fa_path does not exist"; > ! -r _ or croak "$fa_path is not readable"; > $fai = Bio::DB::Sam::Fai->open($fa_path) or croak "$fa_path open: > $!"; > } > > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) 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/devconference > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) 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/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
	Re: [Bioperl-l] Next-gen modules by Cook, Malcolm-2 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Hi Lincoln, I was able to commit the Bio::SamTools patch as http://gmod.svn.sourceforge.net/viewvc/gmod?view=rev&revision=22193 but don't have privs to resolve the issue as fixed here: https://rt.cpan.org/Ticket/ModifyAll.html?id=50532 I note that the subject of where Bio::SamTools bugs/issues should be reports was taken up today by Chris FIelds who asked the group: Just a quick note. We had someone submit a bug to bioperl's bugzilla for Bio::SamTools. I redirected the user to resubmit the bug on the CPAN RT queue for Bio::SamTools, but is there anywhere else they should be directed (eg Sourceforge, etc)? Any advice here? Cheers, Malcolm Cook Stowers Institute for Medical Research - Kansas City, Missouri > -----Original Message----- > From: Scott Cain [mailto:scott@...] > Sent: Friday, October 23, 2009 2:31 PM > To: Cook, Malcolm > Subject: Re: [Gmod-gbrowse] [Bioperl-l] Next-gen modules > > Hi Malcolm, > > I made you a developer; let me know if you need any pointers. > > Scott > > > On Fri, Oct 23, 2009 at 3:18 PM, Cook, Malcolm > <MEC@...> wrote: > > Thanks - Great > > > > userID: 236718 > > user: malcook > > > > > > Malcolm Cook > > Stowers Institute for Medical Research - Kansas City, Missouri > > > > > >> -----Original Message----- > >> From: Scott Cain [mailto:scott@...] > >> Sent: Friday, October 23, 2009 1:18 PM > >> To: Cook, Malcolm > >> Cc: bioperl-l@...; lincoln.stein@...; > >> gmod-gbrowse@...; cain.cshl@... > >> Subject: Re: [Gmod-gbrowse] [Bioperl-l] Next-gen modules > >> > >> Hi Malcolm, > >> > >> You need a SourceForge user account that you'll tell me, so I can > >> give you developer permissions, and then get an svn > checkout of the > >> gbrowse-adaptors repo (we switched to svn last month). > >> > >> Scott > >> > >> > >> On Fri, Oct 23, 2009 at 12:16 PM, Cook, Malcolm <MEC@...> > >> wrote: > >> > Lincoln? Scot? > >> > > >> > Hi there! > >> > > >> > How do I get the permissions I need if Lincoln wants me to > >> submit the > >> > patch below which fixes this bug: > >> > http://rt.cpan.org/Public/Bug/Display.html?id=50532 > >> > > >> > % cvs -d > >> :pserver:anonymous@...:/cvsroot/gmod co > >> > gbrowse-adaptors/Bio-SamTools > >> > > >> > Cheers, > >> > > >> > --Malcolm Cook - Stowers Institute for Medical Research > >> > > >> > > >> > > >> > * Sam.pm.~1.18.~ Thu Sep 24 14:57:53 2009 > >> > --- Sam.pm Fri Oct 23 11:05:14 2009 > >> > *********** > >> > * 1219,1230 **** > >> > my $expand_flags = $args{-expand_flags}; > >> > my $split_splices = $args{-split} \|\| $args{-split_splices}; > >> > > >> > ! -e $bam_path && -r _ or croak "$fa_path does not > exist or is > >> > not readable"; > >> > my $bam = Bio::DB::Bam->open($bam_path) or croak > >> "$bam_path open: > >> > $!"; > >> > > >> > my $fai; > >> > if ($fa_path) { > >> > ! -e $fa_path && -r _ or croak "$fa_path does not > >> exist or is > >> > not readable"; > >> > $fai = Bio::DB::Sam::Fai->open($fa_path) or croak > >> "$fa_path open: > >> > $!"; > >> > } > >> > > >> > --- 1219,1232 ---- > >> > my $expand_flags = $args{-expand_flags}; > >> > my $split_splices = $args{-split} \|\| $args{-split_splices}; > >> > > >> > ! -e $bam_path or croak "$bam_path does not exist"; ! > >> -r _ or > >> > croak "is not readable"; > >> > my $bam = Bio::DB::Bam->open($bam_path) or croak > >> "$bam_path open: > >> > $!"; > >> > > >> > my $fai; > >> > if ($fa_path) { > >> > ! -e $fa_path or croak "$fa_path does not exist"; ! > >> -r _ > >> > or croak "$fa_path is not readable"; > >> > $fai = Bio::DB::Sam::Fai->open($fa_path) or croak > >> "$fa_path open: > >> > $!"; > >> > } > >> > > >> > > >> > > >> > > >> > --------------------------------------------------------------------- > >> - > >> > -------- Come build with us! The BlackBerry(R) 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/devconference > >> > _______________________________________________ > >> > Gmod-gbrowse mailing list > >> > Gmod-gbrowse@... > >> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > >> > > >> > > >> > >> > >> > >> -- > >> -------------------------------------------------------------- > >> ---------- > >> Scott Cain, Ph. D. scott at > >> scottcain dot net GMOD Coordinator (http://gmod.org/) > > >> 216-392-3087 Ontario Institute for Cancer Research > >> > > > > -- > -------------------------------------------------------------- > ---------- > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) 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/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse