Hi Huda,<div><br></div><div>I'm forwarding this to the MAKER dev list to get some more eyes on it. The link to the Korf website works for me. Where are you trying to connect form?</div><div><br></div><div>Mike<br></div>
<br><div class="gmail_quote">On Sun, Feb 10, 2013 at 10:10 PM, Hud Hud <span dir="ltr"><<a href="mailto:hudarul@yahoo.com" target="_blank">hudarul@yahoo.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div style="font-size:12pt;font-family:arial,helvetica,sans-serif"><div><span>Hi Mike,</span></div><div style="font-size:16px;font-family:arial,helvetica,sans-serif;background-color:transparent;font-style:normal"><span style>Thnks 4 ur reply..ive tried the ./Build blast command..I prtscrn the last part of the configuration as attached. Is there anything that I've missed?....And for the SNAP, I tried to download manually from the website, but i cant get access to the </span><span style="color:rgb(0,153,51);font-family:arial,sans-serif;font-size:13px;line-height:15px"><a href="http://korflab.ucdavis.edu/software" target="_blank">korflab.ucdavis.edu/software</a> website.. </span></div>
<div style="color:rgb(0,153,51);font-size:13px;font-family:arial,sans-serif;background-color:transparent;font-style:normal"><br></div><div>Thanks..</div> <div style="font-family:arial,helvetica,sans-serif;font-size:12pt">
<div style="font-family:'times new roman','new york',times,serif;font-size:12pt"> <div dir="ltr"> <font face="Arial"> <hr size="1"><div class="hm HOEnZb"> <b><span style="font-weight:bold">From:</span></b> Michael Campbell <<a href="mailto:michael.s.campbell1@gmail.com" target="_blank">michael.s.campbell1@gmail.com</a>><br>
<b><span style="font-weight:bold">To:</span></b> "李青 Li, Qing" <<a href="mailto:liqing850104@gmail.com" target="_blank">liqing850104@gmail.com</a>> <br><b><span style="font-weight:bold">Cc:</span></b> Hud Hud <<a href="mailto:hudarul@yahoo.com" target="_blank">hudarul@yahoo.com</a>> <br>
<b><span style="font-weight:bold">Sent:</span></b> Monday, February 11, 2013 11:42 AM<br> <b><span style="font-weight:bold">Subject:</span></b> Re: Help on Maker<br> </div></font><div class="hm HOEnZb"> </div></div><div>
<div class="h5"> <br>
<div>Hi Huda,<div><br></div><div>If you have unpacked the maker tar ball and moved to the src directory and have run the "perl <a href="http://build.pl/" target="_blank">Build.PL</a>" command you can run the next command "./Build status" and that should give a report that looks like this.</div>
<div><br></div><div><div>==============================================================================</div><div>STATUS MAKER 2.25</div><div>==============================================================================</div>
<div>PERL Dependencies:<span style="white-space:pre-wrap"> </span>VERIFIED</div><div>External Programs:<span style="white-space:pre-wrap"> </span>VERIFIED</div><div>External C Libraries:<span style="white-space:pre-wrap"> </span>VERIFIED</div>
<div>MPI SUPPORT:<span style="white-space:pre-wrap"> </span>DISABLED</div><div>MWAS Web Interface:<span style="white-space:pre-wrap"> </span>DISABLED</div><div>MAKER PACKAGE:<span style="white-space:pre-wrap"> </span>CONFIGURATION OK</div>
<div><br></div><div><br></div><div>Important Commands:</div><div><span style="white-space:pre-wrap"> </span>./Build installdeps<span style="white-space:pre-wrap"> </span>#installs missing PERL dependencies</div>
<div><span style="white-space:pre-wrap"> </span>./Build installexes<span style="white-space:pre-wrap"> </span>#installs all missing external programs</div><div><span style="white-space:pre-wrap"> </span>./Build install<span style="white-space:pre-wrap"> </span>#installs MAKER</div>
<div><span style="white-space:pre-wrap"> </span>./Build status<span style="white-space:pre-wrap"> </span>#Shows this status menu</div><div><br></div><div>Other Commands:</div><div><span style="white-space:pre-wrap"> </span>./Build repeatmasker<span style="white-space:pre-wrap"> </span>#installs RepeatMasker (asks for RepBase)</div>
<div><span style="white-space:pre-wrap"> </span>.<span style="background-color:rgb(255,255,0)">/Build blast</span><span style="white-space:pre-wrap"> </span>#installs BLAST (NCBI BLAST+)</div>
<div><span style="white-space:pre-wrap"> </span>./Build exonerate<span style="white-space:pre-wrap"> </span>#installs Exonerate (v2 on UNIX / v1 on Mac OSX)</div><div><span style="white-space:pre-wrap"> </span>.<span style="background-color:rgb(255,255,0)">/Build snap</span><span style="white-space:pre-wrap"> </span>#installs SNAP</div>
<div><span style="white-space:pre-wrap"> </span>./Build augustus<span style="white-space:pre-wrap"> </span>#installs Augustus</div><div><span style="white-space:pre-wrap"> </span>./Build apollo<span style="white-space:pre-wrap"> </span>#installs Apollo</div>
<div><span style="white-space:pre-wrap"> </span>./Build gbrowse<span style="white-space:pre-wrap"> </span>#installs GBrowse (must be root)</div><div><span style="white-space:pre-wrap"> </span>./Build jbrowse<span style="white-space:pre-wrap"> </span>#installs JBrowse (MAKER copy, not web accecible)</div>
<div><span style="white-space:pre-wrap"> </span>./Build mpich2<span style="white-space:pre-wrap"> </span>#installs MPICH2 (but manual install recommended)</div></div><div><br></div><div>
<br></div><div>I've highlighted the commands above that you can run to have MAKER install snap and blast for you. Here is a url for a gmod tutorial for installing and running MAKER <a href="http://gmod.org/wiki/MAKER_Tutorial_2012" target="_blank">http://gmod.org/wiki/MAKER_Tutorial_2012</a>.</div>
<div><br></div><div>I haven't actually used cygwin so I am interested in hearing how MAKER runs in that environment. I will ask a few other people and see if they have any experience with cygwin.</div><div><br></div>
<div>
Let me know if you get stuck or have any more questions,</div><div>Mike</div><div><br></div><div><br></div><div>On Sun, Feb 10, 2013 at 6:52 PM, 李青 Li, Qing <span dir="ltr"><<a rel="nofollow" href="mailto:liqing850104@gmail.com" target="_blank">liqing850104@gmail.com</a>></span> wrote:</div>
<div><div><blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello Huda,<div>No worries:) I am cp your question to the expert maker usr in our group!</div>
<div><br></div><div>Mike, would you think you could answer Huda's question and help him, or would you think we need to ask Carlson for help?</div>
<div>Best,</div><div>Qing</div></div><div><div><div><br><br><div>2013/2/10 Hud Hud <span dir="ltr"><<a rel="nofollow" href="mailto:hudarul@yahoo.com" target="_blank">hudarul@yahoo.com</a>></span><br>
<blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="font-size:12pt;font-family:arial,helvetica,sans-serif"><div><div>Hello Hi, Im Huda...Im having problem during the installation of MAKER...I'm not sure whether im asking the right person, I just pick anyone from the list of Yandell People page...Hofefully im not troubling u with this email...</div>
<div>Back to the problem...I try to install Maker but I've noticed that im missing some external program that are Blast and SNAP...how to solve this problem. FYI im very new in this field and not very familiar with programming or scripting. Im using cygwin. Thanks for your help</div>
</div></div></div></blockquote></div><br></div>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Michael Campbell MS, RD.<br>Graduate Student<br>Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330<br>ph:585-3543<br><br>
</div>
</div><br><br> </div></div></div> </div> </div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Michael Campbell MS, RD.<br>Graduate Student<br>Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330<br>ph:585-3543<br><br>