SEA-PHAGES | All posts created by spaudel

Link to this post \| posted 16 May, 2019 17:26
spaudel	Hi Welkin, how do we find appropriate start site if the phage has the serine integrase but can not use the same start as Bxb1? For example Herbertwm_Draft gene 30 (24304 - 25845 ) \| pham 31609.

Posted in: Cluster A Annotation Tips → the start of the integrase

Link to this post \| posted 21 Feb, 2017 21:42
spaudel	Keith Hutchison All of what Kristen has said is good advice. My experience though is that it can get complicated depending on the range of variability of machines: age, MacBook or MacBook Pro, OSX version (Sierra, El Capitan, Yosemite, etc). I do know that on my elderly MacBook what gets install by the 5.30.0 dmg doesn't work. I use the 5.22.23 version from the Baylor site. And that is true for some of my students. Also the version of X11 (XQuartz) that works is also dependent on hardware and/or OS version. The most recent version, 2.7.11 doesn't play well with older machines. My recommendation is that you find someone in IT that not only knows Macs but can work at the command line. Or maybe one of your students could do it. The reason for the latter is that if, in trying to get it to work you students have made several installation attempts, there is some "debris" left from those attempts that needs to be cleared out. Our experience is that it does affect performance. Maybe the last paragraph is all I needed to say. It's not an easy task because the changes needed are variable. At least that's our experience. And more and more students are showing up with Macs. Would you please tell us which file type or files we need to remove from the folder? This package throws an error while blasting.

Link to this post | posted 21 Feb, 2017 21:42

spaudel

Keith Hutchison
All of what Kristen has said is good advice. My experience though is that it can get complicated depending on the range of variability of machines: age, MacBook or MacBook Pro, OSX version (Sierra, El Capitan, Yosemite, etc).

I do know that on my elderly MacBook what gets install by the 5.30.0 dmg doesn't work. I use the 5.22.23 version from the Baylor site. And that is true for some of my students. Also the version of X11 (XQuartz) that works is also dependent on hardware and/or OS version. The most recent version, 2.7.11 doesn't play well with older machines.

My recommendation is that you find someone in IT that not only knows Macs but can work at the command line. Or maybe one of your students could do it. The reason for the latter is that if, in trying to get it to work you students have made several installation attempts, there is some "debris" left from those attempts that needs to be cleared out. Our experience is that it does affect performance.

Maybe the last paragraph is all I needed to say. It's not an easy task because the changes needed are variable. At least that's our experience. And more and more students are showing up with Macs.

Would you please tell us which file type or files we need to remove from the folder? This package throws an error while blasting.

Posted in: DNA Master → Running DNA Master on a Mac using Wine

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All posts created by spaudel