Re: Fate of Bio::Perl newbie module?
Christopher Fields <[email protected]> Mon, 2 Dec 2019 16:11:22 +0000
| Newsgroups | gmane.comp.lang.perl.bio.general |
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| Message-ID | <DM6PR05MB60433F6AAA2E8AE5E10397DBAB430__5260.59123674116$1575303304$gmane$org@DM6PR05MB6043.namprd05.prod.outlook.com> |
--===============0427048634553558935== Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_DM6PR05MB60433F6AAA2E8AE5E10397DBAB430DM6PR05MB6043namp_" --_000_DM6PR05MB60433F6AAA2E8AE5E10397DBAB430DM6PR05MB6043namp_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Not a problem Michael. I also pushed a new Bio::DB::NCBIHelper, which upda= ted a few missing dependencies. chris From: Michael Crusoe <[email protected]> Date: Monday, December 2, 2019 at 10:05 AM To: Andreas Tille <[email protected]> Cc: Chris Fields <[email protected]>, Carn=EB Draug <carandraug+dev@gma= il.com>, Debian Med Project List <[email protected]>, bioperl mai= ling list <[email protected]> Subject: Re: [Bioperl-l] Fate of Bio::Perl newbie module? On Sat, Nov 30, 2019 at 7:32 AM Andreas Tille <[email protected]<mailto:= [email protected]>> wrote: Hi Christopher, On Fri, Nov 29, 2019 at 09:11:41PM +0000, Fields, Christopher J wrote: > Just a quick update: I have pushed a quick release of Bio::DB::SwissProt,= Bio::DB::RefSeq, and Bio::Procedural (which contains Bio::Perl) to CPAN. = I'm awaiting CPAN testing for the Bio::Procedural module (this will show up= here: http://matrix.cpantesters.org/?dist=3DBio-Procedural); the others se= em to be passing. Thanks for the update. I need to admit I personally can not match these modules to the old bioperl package and what might be missing in the new what is needed for reverse dependencies. I've consulted codesearch.debian.net<http://codesearch.debian.net>. I have not found any = reference to Bio::Procedural. Hey Andreas, The Bio-Procedural distribution includes the "Bio::Perl" module: https://me= tacpan.org/pod/Bio::Perl Looks like all the new distributions are live on CPAN, thanks Chris! https://metacpan.org/author/CJFIELDS?sort=3D[[3,1]]<https://metacpan.org/au= thor/CJFIELDS?sort=3D%5b%5b3,1%5d%5d> -- Michael R. Crusoe --_000_DM6PR05MB60433F6AAA2E8AE5E10397DBAB430DM6PR05MB6043namp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable <html xmlns:o=3D"urn:schemas-microsoft-com:office:office" xmlns:w=3D"urn:sc= hemas-microsoft-com:office:word" xmlns:m=3D"http://schemas.microsoft.com/of= fice/2004/12/omml" xmlns=3D"http://www.w3.org/TR/REC-html40"> <head> <meta http-equiv=3D"Content-Type" content=3D"text/html; charset=3Diso-8859-= 1"> <meta name=3D"Generator" content=3D"Microsoft Word 15 (filtered medium)"> <style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; margin-bottom:.0001pt; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} a:visited, span.MsoHyperlinkFollowed {mso-style-priority:99; color:purple; text-decoration:underline;} p.msonormal0, li.msonormal0, div.msonormal0 {mso-style-name:msonormal; mso-margin-top-alt:auto; margin-right:0in; mso-margin-bottom-alt:auto; margin-left:0in; font-size:11.0pt; font-family:"Calibri",sans-serif;} span.EmailStyle18 {mso-style-type:personal-reply; font-family:"Calibri",sans-serif; color:windowtext;} .MsoChpDefault {mso-style-type:export-only; font-size:10.0pt;} @page WordSection1 {size:8.5in 11.0in; margin:1.0in 1.0in 1.0in 1.0in;} div.WordSection1 {page:WordSection1;} --></style> </head> <body lang=3D"EN-US" link=3D"blue" vlink=3D"purple"> <div class=3D"WordSection1"> <p class=3D"MsoNormal">Not a problem Michael. I also pushed a new Bio= ::DB::NCBIHelper, which updated a few missing dependencies. <o:p></o:p></p> <p class=3D"MsoNormal"><o:p> </o:p></p> <p class=3D"MsoNormal">chris<o:p></o:p></p> <p class=3D"MsoNormal"><o:p> </o:p></p> <div style=3D"border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in = 0in 0in"> <p class=3D"MsoNormal"><b><span style=3D"font-size:12.0pt;color:black">From= : </span></b><span style=3D"font-size:12.0pt;color:black">Michael Crusoe &l= t;[email protected]><br> <b>Date: </b>Monday, December 2, 2019 at 10:05 AM<br> <b>To: </b>Andreas Tille <[email protected]><br> <b>Cc: </b>Chris Fields <[email protected]>, Carn=EB Draug <ca= randraug+[email protected]>, Debian Med Project List <debian-med@list= s.debian.org>, bioperl mailing list <[email protected]&g= t;<br> <b>Subject: </b>Re: [Bioperl-l] Fate of Bio::Perl newbie module?<o:p></o:p>= </span></p> </div> <div> <p class=3D"MsoNormal"><o:p> </o:p></p> </div> <div> <div> <p class=3D"MsoNormal"><o:p> </o:p></p> </div> <p class=3D"MsoNormal"><o:p> </o:p></p> <div> <div> <p class=3D"MsoNormal">On Sat, Nov 30, 2019 at 7:32 AM Andreas Tille <<a= href=3D"mailto:[email protected]">[email protected]</a>> wrote:<o= :p></o:p></p> </div> <blockquote style=3D"border:none;border-left:solid #CCCCCC 1.0pt;padding:0i= n 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in"> <p class=3D"MsoNormal">Hi Christopher,<br> <br> On Fri, Nov 29, 2019 at 09:11:41PM +0000, Fields, Christopher J wrote:<= br> > Just a quick update: I have pushed a quick release of Bio::DB::SwissPr= ot, Bio::DB::RefSeq, and Bio::Procedural (which contains Bio::Perl) to CPAN= . I'm awaiting CPAN testing for the Bio::Procedural module (this will= show up here: <a href=3D"http://matrix.cpantesters.org/?dist=3DBio-Procedural" target=3D"= _blank">http://matrix.cpantesters.org/?dist=3DBio-Procedural</a>); the othe= rs seem to be passing. <br> <br> Thanks for the update. I need to admit I personally can not match the= se<br> modules to the old bioperl package and what might be missing in the new<br> what is needed for reverse dependencies. I've consulted<br> <a href=3D"http://codesearch.debian.net" target=3D"_blank">codesearch.debia= n.net</a>. I have not found any reference to<br> Bio::Procedural.<br clear=3D"all"> <o:p></o:p></p> </blockquote> <div> <p class=3D"MsoNormal"><o:p> </o:p></p> </div> <div> <p class=3D"MsoNormal">Hey Andreas,<o:p></o:p></p> </div> <div> <p class=3D"MsoNormal"><o:p> </o:p></p> </div> <div> <p class=3D"MsoNormal">The Bio-Procedural distribution includes the "B= io::Perl" module: <a href=3D"https://metacpan.org/pod/Bio::Perl">https://metacpan.org/pod/Bio= ::Perl</a><o:p></o:p></p> </div> <div> <p class=3D"MsoNormal"><o:p> </o:p></p> </div> <div> <p class=3D"MsoNormal">Looks like all the new distributions are live on CPA= N, thanks Chris!<o:p></o:p></p> </div> <div> <p class=3D"MsoNormal"><o:p> </o:p></p> </div> <div> <p class=3D"MsoNormal"><a href=3D"https://metacpan.org/author/CJFIELDS?sort= =3D%5b%5b3,1%5d%5d">https://metacpan.org/author/CJFIELDS?sort=3D[[3,1]]</a>= <o:p></o:p></p> </div> </div> <p class=3D"MsoNormal"><br> -- <o:p></o:p></p> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <p class=3D"MsoNormal"><span style=3D"font-size:9.5pt">Michael R. Crusoe</s= pan><span style=3D"font-size:12.0pt"><o:p></o:p></span></p> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </body> </html> --_000_DM6PR05MB60433F6AAA2E8AE5E10397DBAB430DM6PR05MB6043namp_-- --===============0427048634553558935== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ Bioperl-l mailing list [email protected] https://mailman.open-bio.org/mailman/listinfo/bioperl-l --===============0427048634553558935==--