Re: Can't find Bio::ext::Align on CPAN
"Fields, Christopher J" <[email protected]> Tue, 16 Mar 2021 15:53:41 +0000
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--===============5806696263183830956== Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_DM6PR11MB4300D17055437856C1D30C82A36B9DM6PR11MB4300namp_" --_000_DM6PR11MB4300D17055437856C1D30C82A36B9DM6PR11MB4300namp_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Correct, quite a few of the tools in that package have not been maintained.= We have discussed releasing some of these as separate packages in the pas= t, but no one has taken this up. chris From: Bioperl-l <[email protected]> on behalf of Mark Jensen <m= [email protected]> Date: Thursday, March 11, 2021 at 9:39 PM To: Warren Gallin <[email protected]> Cc: BioPerl List <[email protected]> Subject: Re: [Bioperl-l] Can't find Bio::ext::Align on CPAN Warren - this is an old module and not currently maintained, but it should = still work. You can find it at https://urldefense.com/v3/__https://github.c= om/bioperl/bioperl-ext__;!!DZ3fjg!uSvOF9SuI7pDulK8EWVNYLGvFzexZNOGo8D4-QUVZ= XWuLtXUoAXqcFQPD2qZMRBq8sA$<https://urldefense.com/v3/__https:/github.com/b= ioperl/bioperl-ext__;!!DZ3fjg!uSvOF9SuI7pDulK8EWVNYLGvFzexZNOGo8D4-QUVZXWuL= tXUoAXqcFQPD2qZMRBq8sA$> There are some details on installation there. Your mileage may vary, but po= st to the list if you run into trouble. Mark Jensen > On Mar 11, 2021, at 5:43 PM, Warren Gallin <[email protected]> wrote: > > I am trying to use the Bio::Tools::dpAlign module, but the run fails with= a message:\ > > The C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has= not been installed. > Please install the bioperl-ext package > > I can not find this package. > > Am I dealing with a no-longer-functional module, or am I missing a pathwa= y to a resource? > > All advice appreciated. > > Warren Gallin_______________________________________________ > Bioperl-l mailing list > [email protected] > https://urldefense.com/v3/__https://mailman.open-bio.org/mailman/listinfo= /bioperl-l__;!!DZ3fjg!uSvOF9SuI7pDulK8EWVNYLGvFzexZNOGo8D4-QUVZXWuLtXUoAXqc= FQPD2qZmrVcpvI$<https://urldefense.com/v3/__https:/mailman.open-bio.org/mai= lman/listinfo/bioperl-l__;!!DZ3fjg!uSvOF9SuI7pDulK8EWVNYLGvFzexZNOGo8D4-QUV= ZXWuLtXUoAXqcFQPD2qZmrVcpvI$> _______________________________________________ Bioperl-l mailing list [email protected] https://urldefense.com/v3/__https://mailman.open-bio.org/mailman/listinfo/b= ioperl-l__;!!DZ3fjg!uSvOF9SuI7pDulK8EWVNYLGvFzexZNOGo8D4-QUVZXWuLtXUoAXqcFQ= PD2qZmrVcpvI$<https://urldefense.com/v3/__https:/mailman.open-bio.org/mailm= an/listinfo/bioperl-l__;!!DZ3fjg!uSvOF9SuI7pDulK8EWVNYLGvFzexZNOGo8D4-QUVZX= WuLtXUoAXqcFQPD2qZmrVcpvI$> --_000_DM6PR11MB4300D17055437856C1D30C82A36B9DM6PR11MB4300namp_ Content-Type: text/html; charset="us-ascii" 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=3Dus-ascii"= > <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; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} span.EmailStyle19 {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" style=3D"word-wrap:brea= k-word"> <div class=3D"WordSection1"> <p class=3D"MsoNormal">Correct, quite a few of the tools in that package ha= ve not been maintained. We have discussed releasing some of these as = separate packages in the past, but no one has taken this up.<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" style=3D"margin-bottom:12.0pt"><b><span style=3D"fon= t-size:12.0pt;color:black">From: </span></b><span style=3D"font-size:12.0pt;color:black">Bioperl-l <biope= [email protected]> on behalf of Mark Jensen <[email protected]= ><br> <b>Date: </b>Thursday, March 11, 2021 at 9:39 PM<br> <b>To: </b>Warren Gallin <[email protected]><br> <b>Cc: </b>BioPerl List <[email protected]><br> <b>Subject: </b>Re: [Bioperl-l] Can't find Bio::ext::Align on CPAN<o:p></o:= p></span></p> </div> <div> <p class=3D"MsoNormal">Warren - this is an old module and not currently mai= ntained, but it should still work. You can find it at <a href=3D"https://urldefense.com/v3/__https:/github.com/bioperl/bioperl-ex= t__;!!DZ3fjg!uSvOF9SuI7pDulK8EWVNYLGvFzexZNOGo8D4-QUVZXWuLtXUoAXqcFQPD2qZMR= Bq8sA$"> https://urldefense.com/v3/__https://github.com/bioperl/bioperl-ext__;!!DZ3f= jg!uSvOF9SuI7pDulK8EWVNYLGvFzexZNOGo8D4-QUVZXWuLtXUoAXqcFQPD2qZMRBq8sA$</a> <br> There are some details on installation there. Your mileage may vary, but po= st to the list if you run into trouble.<br> <br> Mark Jensen<br> <br> > On Mar 11, 2021, at 5:43 PM, Warren Gallin <[email protected]>= wrote:<br> > <br> > I am trying to use the Bio::Tools::dpAlign module, but the run fails w= ith a message:\<br> > <br> > The C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) = has not been installed.<br> > Please install the bioperl-ext package<br> > <br> > I can not find this package.<br> > <br> > Am I dealing with a no-longer-functional module, or am I missing a pat= hway to a resource?<br> > <br> > All advice appreciated.<br> > <br> > Warren Gallin_______________________________________________<br> > Bioperl-l mailing list<br> > [email protected]<br> > <a href=3D"https://urldefense.com/v3/__https:/mailman.open-bio.org/mai= lman/listinfo/bioperl-l__;!!DZ3fjg!uSvOF9SuI7pDulK8EWVNYLGvFzexZNOGo8D4-QUV= ZXWuLtXUoAXqcFQPD2qZmrVcpvI$"> https://urldefense.com/v3/__https://mailman.open-bio.org/mailman/listinfo/b= ioperl-l__;!!DZ3fjg!uSvOF9SuI7pDulK8EWVNYLGvFzexZNOGo8D4-QUVZXWuLtXUoAXqcFQ= PD2qZmrVcpvI$</a> <br> <br> _______________________________________________<br> Bioperl-l mailing list<br> [email protected]<br> <a href=3D"https://urldefense.com/v3/__https:/mailman.open-bio.org/mailman/= listinfo/bioperl-l__;!!DZ3fjg!uSvOF9SuI7pDulK8EWVNYLGvFzexZNOGo8D4-QUVZXWuL= tXUoAXqcFQPD2qZmrVcpvI$">https://urldefense.com/v3/__https://mailman.open-b= io.org/mailman/listinfo/bioperl-l__;!!DZ3fjg!uSvOF9SuI7pDulK8EWVNYLGvFzexZN= OGo8D4-QUVZXWuLtXUoAXqcFQPD2qZmrVcpvI$</a> <o:p></o:p></p> </div> </div> </body> </html> --_000_DM6PR11MB4300D17055437856C1D30C82A36B9DM6PR11MB4300namp_-- --===============5806696263183830956== 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 --===============5806696263183830956==--