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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Ok... <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal style='margin-left:36.0pt'><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org] <b>On Behalf Of </b>Will McLaren<br><b>Sent:</b> 27 November 2012 13:31<br><b>To:</b> Ensembl developers list<br><b>Subject:</b> Re: [ensembl-dev] How to disable the fork in plugins in the vep script<o:p></o:p></span></p></div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Hi Duarte,<o:p></o:p></p><div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'>Your new method should contain something like this:<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div><div><div><p class=MsoNormal style='margin-left:36.0pt'>sub new {<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'> my $class = shift;<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'> my $self = $class->SUPER::new(@_);<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'> <o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'> delete $self->{config}->{fork} if defined($self->{config}->{fork});<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'> return $self;<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'>}<o:p></o:p></p></div></div><div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'>Note that this will disable forking globally (i.e. the same as if you had not added --fork on the command line).<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'>Will<o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt'><o:p> </o:p></p><div><p class=MsoNormal style='margin-left:36.0pt'>On 27 November 2012 13:23, Duarte Molha <<a href="mailto:Duarte.Molha@ogt.co.uk" target="_blank">Duarte.Molha@ogt.co.uk</a>> wrote:<o:p></o:p></p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>Dear developers<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>The use of fork seems to crash the script and I would like to test disabling the fork for my plugins.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>In your documentation you say:<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'><b><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:#555555;background:white'>NB:</span></b><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:#555555;background:white'> VEP users writing plugins should be aware that while the VEP code attempts to preserve the state of any plugin-specific cached data between separate forks, there may be situations where data is lost. If you find this is the case, you should disable forking in the new() method of your plugin by deleting the "fork" key from the $config hash.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:#555555;background:white'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>Can you specify exactly how you would to this?<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>Cheers, <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Duarte Molha</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p></div></div><p class=MsoNormal style='mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt'><br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><o:p></o:p></p></div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div></div></body></html>