<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi Tim,
<div class="">Thanks again for doing this. I’ve installed stacks web but got some errors (below) when attempting to create the database. I’m not familiar with how it works so not sure if this is a problem?</div>
<div class=""><br class="">
</div>
<div class="">Thanks,</div>
<div class=""><br class="">
</div>
<div class="">Simon</div>
<div class="">
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">simonw@PowerEdge-R820[simonw] sudo stacks-setup-database gweedall [ 7:26PM]</div>
<div class="">ERROR 1045 (28000): Access denied for user 'debian-sys-maint'@'localhost' (using password: YES)</div>
<div class="">Making database gweedall_radtags for gweedall</div>
<div class="">ERROR 1045 (28000): Access denied for user 'debian-sys-maint'@'localhost' (using password: YES)</div>
<div class="">Aborting.</div>
<div class="">simonw@PowerEdge-R820[simonw] [ 7:27PM]</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div apple-content-edited="true" class=""><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px;">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<font class="Apple-style-span" size="2">_________________________________</font></div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<font class="Apple-style-span" size="2"><br class="">
</font></div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<font class="Apple-style-span" size="2">Simon Wagstaff<br class="">
Tel: +44-(0)151-705-3164<br class="">
Fax: +44-(0)151-705-3371<br class="">
email: <a href="mailto:simon.wagstaff@lstmed.ac.uk" class="">simon.wagstaff@lstmed.ac.uk</a><br class="">
<br class="">
<br class="">
</font><br class="">
</div>
</span></div>
</span></div>
</span></div>
</span></div>
</span></div>
</span></div>
</span></div>
</span></div>
</span></div>
<br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 23 Jan 2015, at 14:39, Tim Booth <<a href="mailto:tbooth@ceh.ac.uk" class="">tbooth@ceh.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Hi All,<br class="">
<br class="">
A very long time ago, someone asked me if I could put Stacks<br class="">
(<a href="http://creskolab.uoregon.edu/stacks/" class="">http://creskolab.uoregon.edu/stacks/</a>) on Bio-Linux. More recently,<br class="">
other people have asked more insistently if I can do a package, and I<br class="">
finally have.<br class="">
<br class="">
So you can "apt-get install stacks" then type:<br class="">
<br class="">
$ stacks help<br class="">
<br class="">
To see available commands.<br class="">
<br class="">
There are various problems with getting Stacks to work well as a<br class="">
package, especially the database and web viewer bit, which I've split<br class="">
into a package called "stacks-web". The standard installation is both<br class="">
really complex and assumes that you are the sole user on the system, or<br class="">
at least that you don't care about other users accessing all your stuff.<br class="">
I think I've made things much neater and simpler, but the upshot is that<br class="">
most of the regular set-up instructions are misleading for anyone using<br class="">
this new package. Essentially there is now just one thing to do -<br class="">
running:<br class="">
<br class="">
$ sudo stacks-setup-database <username><br class="">
<br class="">
Before that particular user tries to load anything to the database.<br class="">
<br class="">
If you are interested in using Stacks please let me know if you try<br class="">
these packages, and let me know if they actually work or if you have any<br class="">
problems/questions.<br class="">
<br class="">
Cheers,<br class="">
<br class="">
TIM<br class="">
<br class="">
-- <br class="">
Tim Booth <<a href="mailto:tbooth@ceh.ac.uk" class="">tbooth@ceh.ac.uk</a>><br class="">
NERC Environmental Bioinformatics Centre <br class="">
<br class="">
Centre for Ecology and Hydrology<br class="">
Maclean Bldg, Benson Lane<br class="">
Crowmarsh Gifford<br class="">
Wallingford, England<br class="">
OX10 8BB <br class="">
<br class="">
<a href="http://environmentalomics.org/bio-linux" class="">http://environmentalomics.org/bio-linux</a><br class="">
+44 1491 69 2297<br class="">
<br class="">
_______________________________________________<br class="">
Bio-Linux mailing list<br class="">
Bio-Linux@nebclists.nerc.ac.uk<br class="">
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux<br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
<hr>
<p style="font: 8pt calibri; color:black;"></p>
<img src="http://www.lstmed.ac.uk/images/lstm_email_logo.gif">
<p style="font: 8pt calibri; color:black;">This e-mail message is sent on behalf of the Liverpool School of Tropical Medicine, a charitable company limited by guarantee registered in England and Wales with company number 222655 and whose registered office is
at Pembroke Place Liverpool L3 5QA ("LSTM")</p>
<p style="font: 8pt calibri; color:black;">The contents of this e-mail are subject to LSTM’s email disclaimer found at:<br>
<a href="http://www.lstmed.ac.uk/disclaimer/email-disclaimer">http://www.lstmed.ac.uk/disclaimer/email-disclaimer</a>
</p>
</body>
</html>