<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 12 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@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;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","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.MsoAcetate, li.MsoAcetate, div.MsoAcetate
{mso-style-priority:99;
mso-style-link:"Balloon Text Char";
margin:0cm;
margin-bottom:.0001pt;
font-size:8.0pt;
font-family:"Tahoma","sans-serif";}
span.EmailStyle17
{mso-style-type:personal;
font-family:"Calibri","sans-serif";
color:#1F497D;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
span.BalloonTextChar
{mso-style-name:"Balloon Text Char";
mso-style-priority:99;
mso-style-link:"Balloon Text";
font-family:"Tahoma","sans-serif";}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</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'>Here is the output for the failed process<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><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>Duarte Molha<br><b>Sent:</b> 27 November 2012 14:53<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></div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I am still having issues with using the fork parameter.<o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>The script seems to die a bit randomly<o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I run it once with 3 forks and outputting the default annotation in tab delimited format<o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>When I tried running exactly the same command but this time outputting to vfc the script dies with the message<o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>“ERROR: Forked process failed”<o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Still have not been able to determine the reason for this. <o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Anyone else has had a similar issue?<o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Cheers<o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Duarte<o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><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:72.0pt'><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"'> <a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a> [<a href="mailto:dev-bounces@ensembl.org">mailto:dev-bounces@ensembl.org</a>] <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:72.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:72.0pt'>Hi Duarte,<o:p></o:p></p><div><p class=MsoNormal style='margin-left:72.0pt'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:72.0pt'>Your new method should contain something like this:<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:72.0pt'><o:p> </o:p></p></div><div><div><p class=MsoNormal style='margin-left:72.0pt'>sub new {<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:72.0pt'> my $class = shift;<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:72.0pt'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:72.0pt'> my $self = $class->SUPER::new(@_);<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:72.0pt'> <o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:72.0pt'> delete $self->{config}->{fork} if defined($self->{config}->{fork});<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:72.0pt'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:72.0pt'> return $self;<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:72.0pt'>}<o:p></o:p></p></div></div><div><p class=MsoNormal style='margin-left:72.0pt'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:72.0pt'>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:72.0pt'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:72.0pt'>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:72.0pt'><o:p> </o:p></p><div><p class=MsoNormal style='margin-left:72.0pt'>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:72.0pt'>Dear developers<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt'>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:72.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt'>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:72.0pt'><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:72.0pt'><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:72.0pt'>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:72.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt'>Cheers, <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt'><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:72.0pt'> <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:72.0pt'><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:72.0pt'><o:p> </o:p></p></div></div></body></html>