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Re: [Gmod-ajax] JBrowse not installing: perl prerequisites issue
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From: Scott C. <sc...@sc...> - 2024-10-22 15:39:34
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<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div dir="ltr"></div><div dir="ltr">Hi Vaneet,</div><div dir="ltr"><br></div><div dir="ltr">What are you planning on using the VM for? If it’s only for serving JBrowse (and not processing data files), you can do what I did in the wormbase docker file and use the “-f” option for the setup script that causes it to skip installing the Perl prereqs:</div><div dir="ltr"><br></div><div dir="ltr"><div style="display: block;" class=""><div style="-webkit-user-select: all; -webkit-user-drag: element; display: inline-block;" class="apple-rich-link" draggable="true" role="link" data-url="https://github.com/WormBase/website-genome-browsers/blob/jbrowse-279/jbrowse/Dockerfile"><a style="border-radius:10px;font-family:-apple-system, Helvetica, Arial, sans-serif;display:block;-webkit-user-select:none;width:300px;user-select:none;-webkit-user-modify:read-only;user-modify:read-only;overflow:hidden;text-decoration:none;" class="lp-rich-link" rel="nofollow" href="https://github.com/WormBase/website-genome-browsers/blob/jbrowse-279/jbrowse/Dockerfile" dir="ltr" role="button" draggable="false" width="300"><table style="table-layout:fixed;border-collapse:collapse;width:300px;background-color:#E6E6E6;font-family:-apple-system, Helvetica, Arial, sans-serif;" class="lp-rich-link-emailBaseTable" cellpadding="0" cellspacing="0" border="0" width="300"><tbody><tr><td vertical-align="center" align="center"><img style="width:300px;filter:brightness(0.97);height:150px;" width="300" height="150" draggable="false" class="lp-rich-link-mediaImage" alt="website-genome-browsers.png" src="cid:684571C5-8664-408B-87F1-4D50DA97DFAB"></td></tr><tr><td vertical-align="center"><table bgcolor="#E6E6E6" cellpadding="0" cellspacing="0" width="300" style="table-layout:fixed;font-family:-apple-system, Helvetica, Arial, sans-serif;background-color:rgba(230, 230, 230, 1);-apple-color-filter:initial;" class="lp-rich-link-captionBar"><tbody><tr><td style="padding:8px 0px 8px 0px;" class="lp-rich-link-captionBar-textStackItem"><div style="max-width:100%;margin:0px 16px 0px 16px;overflow:hidden;" class="lp-rich-link-captionBar-textStack"><div style="word-wrap:break-word;font-weight:500;font-size:12px;overflow:hidden;text-overflow:ellipsis;text-align:left;" class="lp-rich-link-captionBar-textStack-topCaption-leading"><a rel="nofollow" href="https://github.com/WormBase/website-genome-browsers/blob/jbrowse-279/jbrowse/Dockerfile" style="text-decoration: none" draggable="false"><font color="#000000" style="color: rgba(0, 0, 0, 1);">website-genome-browsers/jbrowse/Dockerfile at jbrowse-279 · WormBase/website-genome-browsers</font></a></div><div style="word-wrap:break-word;font-weight:400;font-size:11px;overflow:hidden;text-overflow:ellipsis;text-align:left;" class="lp-rich-link-captionBar-textStack-bottomCaption-leading"><a rel="nofollow" href="https://github.com/WormBase/website-genome-browsers/blob/jbrowse-279/jbrowse/Dockerfile" style="text-decoration: none" draggable="false"><font color="#A2A2A9" style="color: rgba(60, 60, 67, 0.6);">github.com</font></a></div></div></td></tr></tbody></table></td></tr></tbody></table></a></div></div><br></div><div dir="ltr">On the other hand, if you plan on using the vm for doing data processing and thus need Perl, you can look at the Dockerfile I created for doing just that at:</div><div dir="ltr"><br></div><div dir="ltr"><div style="display: block;" class=""><div style="-webkit-user-select: all; -webkit-user-drag: element; display: inline-block;" class="apple-rich-link" draggable="true" role="link" data-url="https://github.com/alliance-genome/agr_jbrowse_container/blob/master/Dockerfile.processenv"><a style="border-radius:10px;font-family:-apple-system, Helvetica, Arial, sans-serif;display:block;-webkit-user-select:none;width:300px;user-select:none;-webkit-user-modify:read-only;user-modify:read-only;overflow:hidden;text-decoration:none;" class="lp-rich-link" rel="nofollow" href="https://github.com/alliance-genome/agr_jbrowse_container/blob/master/Dockerfile.processenv" dir="ltr" role="button" draggable="false" width="300"><table style="table-layout:fixed;border-collapse:collapse;width:300px;background-color:#E6E6E6;font-family:-apple-system, Helvetica, Arial, sans-serif;" class="lp-rich-link-emailBaseTable" cellpadding="0" cellspacing="0" border="0" width="300"><tbody><tr><td vertical-align="center" align="center"><img style="width:300px;filter:brightness(0.97);height:150px;" width="300" height="150" draggable="false" class="lp-rich-link-mediaImage" alt="agr_jbrowse_container.png" src="cid:9926C247-3CEA-4B8A-BB05-F2B7F10CF0E4"></td></tr><tr><td vertical-align="center"><table bgcolor="#E6E6E6" cellpadding="0" cellspacing="0" width="300" style="table-layout:fixed;font-family:-apple-system, Helvetica, Arial, sans-serif;background-color:rgba(230, 230, 230, 1);-apple-color-filter:initial;" class="lp-rich-link-captionBar"><tbody><tr><td style="padding:8px 0px 8px 0px;" class="lp-rich-link-captionBar-textStackItem"><div style="max-width:100%;margin:0px 16px 0px 16px;overflow:hidden;" class="lp-rich-link-captionBar-textStack"><div style="word-wrap:break-word;font-weight:500;font-size:12px;overflow:hidden;text-overflow:ellipsis;text-align:left;" class="lp-rich-link-captionBar-textStack-topCaption-leading"><a rel="nofollow" href="https://github.com/alliance-genome/agr_jbrowse_container/blob/master/Dockerfile.processenv" style="text-decoration: none" draggable="false"><font color="#000000" style="color: rgba(0, 0, 0, 1);">agr_jbrowse_container/Dockerfile.processenv at master · alliance-genome/agr_jbrowse_container</font></a></div><div style="word-wrap:break-word;font-weight:400;font-size:11px;overflow:hidden;text-overflow:ellipsis;text-align:left;" class="lp-rich-link-captionBar-textStack-bottomCaption-leading"><a rel="nofollow" href="https://github.com/alliance-genome/agr_jbrowse_container/blob/master/Dockerfile.processenv" style="text-decoration: none" draggable="false"><font color="#A2A2A9" style="color: rgba(60, 60, 67, 0.6);">github.com</font></a></div></div></td></tr></tbody></table></td></tr></tbody></table></a></div></div><br></div><div dir="ltr">Which installs an old JBrowse release (because I only need the processing scripts so it didn’t matter what version I installed) but this could help with your installation woes. </div><div dir="ltr"><br></div><div dir="ltr">Finally, I’ll say I much prefer separating what vm processes that data versus the vm that serves the data up in JBrowse (made easier by putting the data on a third server like AWS S3) because it makes building issues like these easier to deal with. </div><div dir="ltr"><br></div><div dir="ltr">One more thing and I’ll stop: I don’t know if you use AWS, but another option you might consider for serving up JBrowse is to skip the VM altogether and use Amplify, which is what I currently use for WormBase and JBrowse 1:</div><div dir="ltr"><br></div><div dir="ltr"><div style="display: block;" class=""><div style="-webkit-user-select: all; -webkit-user-drag: element; display: inline-block;" class="apple-rich-link" draggable="true" role="link" data-url="https://github.com/WormBase/amplify-wb-jbrowse1"><a style="border-radius:10px;font-family:-apple-system, Helvetica, Arial, sans-serif;display:block;-webkit-user-select:none;width:300px;user-select:none;-webkit-user-modify:read-only;user-modify:read-only;overflow:hidden;text-decoration:none;" class="lp-rich-link" rel="nofollow" href="https://github.com/WormBase/amplify-wb-jbrowse1" dir="ltr" role="button" draggable="false" width="300"><table style="table-layout:fixed;border-collapse:collapse;width:300px;background-color:#DDDDDD;font-family:-apple-system, Helvetica, Arial, sans-serif;" class="lp-rich-link-emailBaseTable" cellpadding="0" cellspacing="0" border="0" width="300"><tbody><tr><td vertical-align="center"><table bgcolor="#DDDDDD" cellpadding="0" cellspacing="0" width="300" style="table-layout:fixed;font-family:-apple-system, Helvetica, Arial, sans-serif;background-color:rgba(221, 221, 221, 1);-apple-color-filter:initial;" class="lp-rich-link-captionBar"><tbody><tr><td style="padding:8px 0px 8px 0px;" class="lp-rich-link-captionBar-textStackItem"><div style="max-width:100%;margin:0px 16px 0px 16px;overflow:hidden;" class="lp-rich-link-captionBar-textStack"><div style="word-wrap:break-word;font-weight:500;font-size:12px;overflow:hidden;text-overflow:ellipsis;text-align:left;" class="lp-rich-link-captionBar-textStack-topCaption-leading"><a rel="nofollow" href="https://github.com/WormBase/amplify-wb-jbrowse1" style="text-decoration: none" draggable="false"><font color="#000000" style="color: rgba(0, 0, 0, 1);">WormBase/amplify-wb-jbrowse1: Repo to drive AWS Amplify builds for JBrowse 1</font></a></div><div style="word-wrap:break-word;font-weight:400;font-size:11px;overflow:hidden;text-overflow:ellipsis;text-align:left;" class="lp-rich-link-captionBar-textStack-bottomCaption-leading"><a rel="nofollow" href="https://github.com/WormBase/amplify-wb-jbrowse1" style="text-decoration: none" draggable="false"><font color="#A2A2A9" style="color: rgba(60, 60, 67, 0.6);">github.com</font></a></div></div></td><td style="padding:6px 12px 6px 0px;" class="lp-rich-link-captionBar-rightIconItem" width="30"><a rel="nofollow" href="https://github.com/WormBase/amplify-wb-jbrowse1" draggable="false"><img style="pointer-events:none !important;display:inline-block;width:30px;height:30px;border-radius:3px;" width="30" height="30" draggable="false" class="lp-rich-link-captionBar-rightIcon" alt="apple-touch-icon-180x180-a80b8e11abe2.png" src="cid:8FA10AE9-EDD1-4E77-80A8-273E818BDFB2"></a></td></tr></tbody></table></td></tr></tbody></table></a></div></div><br></div><div dir="ltr">This is a slightly odd example, since it’s really serving two side by side instances of JBrowse, but since the /dist directory is already built, it doesn’t need to build JBrowse at all, I just update the trackList.json files and the JBrowse instance automatically rebuilds (again, with the data being already processed somewhere else).</div><div dir="ltr"><br></div><div dir="ltr">Scott</div><div dir="ltr"><br></div><div dir="ltr"><br><blockquote type="cite">On Oct 22, 2024, at 6:00 AM, Colin <col...@gm...> wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr"><p dir="ltr">can you attach the setup.log file?</p> <br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Oct 22, 2024, 3:36 AM Vaneet Lotay <<a href="mailto:van...@uc...">van...@uc...</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <div dir="ltr"> <p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Hello,</span></p> <p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"> </span></p> <p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">I’m installing JBrowse on a new Ubuntu VM. I already heeded the previous advice to use Node.js v14 as later versions were in fact causing the usual ‘node-sass’ issue. Even though I have python3 installed, I had to install python2 since the setup script was looking for it and would fail without it. Anyways now when I run the setup script, my Perl prerequisites fail to install:</span></p> <p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"> </span></p> <p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><i>Installing Perl prerequisites ... failed. See setup.log file for error messages. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.</i></span></p> <p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><i> </i></span></p> <p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><i>Formatting Volvox example data ... failed. See setup.log file for error messages.</i></span></p> <p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"> </span></p> <p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">I did in fact install the system prerequisites using this command:</span></p> <p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"> </span></p> <p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">apt install build-essential zlib1g-dev</span></p> <p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"> </span></p> <p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Not sure if that’s what it’s looking for but nevertheless when executing that command now it indicates I have the latest version for all these packages. I'd be happy to attach my setup.log file too directly, I just can't post it to the mailing list as it seems too big for the limit.</span></p> <p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"> </span></p> <p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Thanks for any help you can provide!</span></p> <p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"> </span></p> <p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Vaneet</span></p> <div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"> <br> </div> </div> _______________________________________________<br> Gmod-ajax mailing list<br> <a href="mailto:Gmo...@li..." target="_blank" rel="noreferrer">Gmo...@li...</a><br> <a href="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" rel="noreferrer noreferrer" target="_blank">https://lists.sourceforge.net/lists/listinfo/gmod-ajax</a><br> </blockquote></div> <span>_______________________________________________</span><br><span>Gmod-ajax mailing list</span><br><span>Gmo...@li...</span><br><span>https://lists.sourceforge.net/lists/listinfo/gmod-ajax</span><br></div></blockquote></body></html> |
