<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>Some files it can reuse, but not all. So, exporting finished contigs with GFF3 pass-through is an option.</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Daniel Hughes <<a href="mailto:dsth@ebi.ac.uk">dsth@ebi.ac.uk</a>><br><span style="font-weight:bold">Date: </span> Monday, 4 March, 2013 3:57 PM<br><span style="font-weight:bold">To: </span> Kenlee Nakasugi <<a href="mailto:kenlee.nakasugi@sydney.edu.au">kenlee.nakasugi@sydney.edu.au</a>><br><span style="font-weight:bold">Cc: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a> List" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>>, Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] regarding mpich<br></div><div><br></div><p>Unlikely. Probably safer to export what has finished as gff and run it as re-annotation if you don't want to waste what was alteady processed for running additional iterations. </p><p>Dan</p><p>from me phone...</p><div class="gmail_quote">On Mar 4, 2013 8:52 PM, "Kenlee Nakasugi" <<a href="mailto:kenlee.nakasugi@sydney.edu.au">kenlee.nakasugi@sydney.edu.au</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div bgcolor="#FFFFFF"><div>Thanks Carson. Will Maker 2.27 be able to continue analysis on Maker 2.1 files that stopped halfway? </div><div>Thanks</div><div>Ken<br><br><br></div><div><br>
On 05/03/2013, at 1:44 AM, "Carson Holt" <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>> wrote:<br><br></div><div></div><blockquote type="cite"><div><div>Use the last MPICH2 version, as MPICH3 is very different (it's the first attempt to implement the new MPI3 protocol set, and not just a version update). Alternatively you can use OpenMPI. Also use maker version 2.27 instead for MPI.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none"><span style="font-weight:bold">From: </span>Kenlee Nakasugi <<a href="mailto:kenlee.nakasugi@sydney.edu.au" target="_blank">kenlee.nakasugi@sydney.edu.au</a>><br><span style="font-weight:bold">Date: </span>Sunday, 3 March, 2013 6:44 PM<br><span style="font-weight:bold">To: </span>"<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a> List" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span>[maker-devel] regarding mpich<br></div><div><br></div><div><div>Hi, <br><br>
I'm trying to install mpi_maker (Maker 2.1) on a new system (intel ix x86_64) which has mpich v3.0.2 installed, but I can't seem to get maker Build.PL to recognize it. I tried editing the Build.pm file to point to it, but with no success.
<br>
All dependencies have been installed and successfully recognized, it is just MPI support that is not.
<br><br>
Is there anything I could modify in the install scripts to make it recognize this? Currently, the directly path to where the mpicc and mpiexec are is /apps/mpich/3.0.2/bin<br>
I don't have sys admin rights for the machine, and I'm not sure if this version of mpich was installed for shared libraries as per the GMOD tutorial. But I have previously circumvented this with an earlier version of mpich by modifying the Build.pm module with
success. I'm wondering if mpichv3.02 is not compatible? <br><br><br>
Cheers, <br>
Ken<br><br><table cellspacing="0" cellpadding="0" width="100%"><tbody><tr><td><pre>--
Kenlee Nakasugi | Research Fellow
School of Molecular Bioscience
Level 8, SMB Building (G08)| The University of Sydney | NSW | 2006
T: <a href="tel:%2B61%202%209114%201321" value="+61291141321" target="_blank">+61 2 9114 1321</a>
E: <a href="mailto:kenlee.nakasugi@sydney.edu.au" target="_blank">kenlee.nakasugi@sydney.edu.au</a></pre></td></tr></tbody></table></div></div>
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