SEA-PHAGES | All posts created by kbutela

Link to this post \| posted 15 Feb, 2016 19:35
kbutela	Is anyone still using the cluster specific primers to assign mycobacteriophages to various clusters? I have some students who may be interested in screening some unsequenced phages we have in our archive, but I haven't been able to find the list. I'd like to spend some time on PCR and gel electrophoresis this semester, and I thought this may be an option. Is this still a useful protocol, or have we moved on to something else?

Link to this post | posted 15 Feb, 2016 19:35

Is anyone still using the cluster specific primers to assign mycobacteriophages to various clusters? I have some students who may be interested in screening some unsequenced phages we have in our archive, but I haven't been able to find the list. I'd like to spend some time on PCR and gel electrophoresis this semester, and I thought this may be an option. Is this still a useful protocol, or have we moved on to something else?

Posted in: Phage Discovery/Isolation → Cluster Specific Primers

Link to this post \| posted 04 Feb, 2016 03:40
kbutela	I just heard back from students using OSX 10.9.5 and 10.10.5. Both are still getting the OLE error when attempting to BLAST. Both students are using an old DNA Master build with XQuartz 2.7.6. I have no explanations at this point. However, I just posted a separate thread on running DNA Master on the SEA Ubuntu Virtual Machine. I was successful at this attempt, and I am now able to run a mostly fully functional version of DNA Master directly on the VM. I do not get any errors when using BLAST.

Link to this post | posted 04 Feb, 2016 03:40

kbutela

I just heard back from students using OSX 10.9.5 and 10.10.5. Both are still getting the OLE error when attempting to BLAST. Both students are using an old DNA Master build with XQuartz 2.7.6. I have no explanations at this point.

However, I just posted a separate thread on running DNA Master on the SEA Ubuntu Virtual Machine. I was successful at this attempt, and I am now able to run a mostly fully functional version of DNA Master directly on the VM. I do not get any errors when using BLAST.

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

Link to this post \| posted 04 Feb, 2016 03:37
kbutela	After several agonizing hours and an incredibly steep learning curve, I am now running DNA Master on the SEA Virtual Machine. I am able to BLAST without getting the OLE error that my students are getting on the Mac WINE version. If this is something others are interested in, I will create a Screenflow for installation and use.

Posted in: DNA Master → Running DNA Master on the Ubuntu SEA Virtual Machine

Link to this post \| posted 03 Feb, 2016 21:08
kbutela	I should also note that I received the BLAST OLE error when using the updated Baylor package (latest DNA Master update) link with OSX 10.9.5 and XQuartz 2.7.6. Maybe it's also a problem with the latest DNA Master update?

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

Link to this post \| posted 03 Feb, 2016 21:07
kbutela	I am currently able to successfully BLAST using the following parameters: OSX 10.9.5 XQuartz 2.7.6 DNA Master WINE package 5.22.15 with last update January 2015 My students are all on Macs ranging from 10.9.4 to El Capitan (11.3.1, I think). I directed all of them to install XQuartz 2.7.6 and the DNA Master WINE package 5.22.15 with last update January 2015. We just finished installing the same software configuration on everyone's computers, so I will have BLAST updates later this evening hopefully. I'm wondering if the BLAST OLE error is resulting from a combination of issues with DNA Master and XQuartz.

Link to this post | posted 03 Feb, 2016 21:07

kbutela

I am currently able to successfully BLAST using the following parameters:

OSX 10.9.5
XQuartz 2.7.6
DNA Master WINE package 5.22.15 with last update January 2015

My students are all on Macs ranging from 10.9.4 to El Capitan (11.3.1, I think).
I directed all of them to install XQuartz 2.7.6 and the DNA Master WINE package 5.22.15 with last update January 2015.

We just finished installing the same software configuration on everyone's computers, so I will have BLAST updates later this evening hopefully. I'm wondering if the BLAST OLE error is resulting from a combination of issues with DNA Master and XQuartz.

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

Link to this post \| posted 02 Feb, 2016 20:54
kbutela	I should also note that our university has advised us NOT to upgrade to El Capitan, so I'm still on the OSX 10.9.5

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

Link to this post \| posted 02 Feb, 2016 20:53
kbutela	I'm wondering if it's a problem with XQuartz/X11. I'm running 2.7.6 and all is well on my end. I just ran a successful BLAST during peak hours with no error message. Results saved to database.

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

Link to this post \| posted 02 Feb, 2016 19:09
kbutela	I uploaded the file to my Google Drive. Anyone with the link should be able to download the file. https://drive.google.com/open?id=0B7VOsLplKJxoeGx3ZGJ3WFFqY28

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

Link to this post \| posted 02 Feb, 2016 14:39
kbutela	Tamarah Adair Today I received a few inquiries about using the DNAMaster in WINE. The link that is posted should still work. This is the comment I have from our IT- Users can download the box version and run it and it will update itself as usual. Once the updates have ran, that user will have the equivalent of what is in G42. We are using this version- but we are not able to BLAST from DNAMAster. I am getting a directory (?) error after a few minutes that says OLE error. Does anyone have any ideas on how to fix this? We can use the NCBI and phagesdb sites for annotation, but eventually we are going to need to have BLAST results in DNAMaster. Theoretically, this version is detecting DNAMaster updates, but I am wondering if there is a new link out to NCBI that it is not seeing? We are running DNA Master within the WINE configuration. The installer has been copied and you should be able to get to it from this link. https://baylor.box.com/s/295to06pr1cpztqiu2jn0h77iy3vkanz THANKS! I also encountered this problem when I used the newest DNA Master WINE build from the Baylor site. I was able to work around the issue by going back to an older version of DNA Master-WINE that I downloaded from the Baylor site last year. I updated DNA Master from within the program to the latest version, and I am able to use BLAST successfully. I'm thinking there is something wrong with the latest version of WINE itself, giving the OLE error?

Link to this post | posted 02 Feb, 2016 14:39

kbutela

Tamarah Adair
Today I received a few inquiries about using the DNAMaster in WINE. The link that is posted should still work. This is the comment I have from our IT-
Users can download the box version and run it and it will update itself as usual. Once the updates have ran, that user will have the equivalent of what is in G42.

We are using this version- but we are not able to BLAST from DNAMAster. I am getting a directory (?) error after a few minutes that says OLE error. Does anyone have any ideas on how to fix this? We can use the NCBI and phagesdb sites for annotation, but eventually we are going to need to have BLAST results in DNAMaster. Theoretically, this version is detecting DNAMaster updates, but I am wondering if there is a new link out to NCBI that it is not seeing?
We are running DNA Master within the WINE configuration.
The installer has been copied and you should be able to get to it from this link.
https://baylor.box.com/s/295to06pr1cpztqiu2jn0h77iy3vkanz

THANKS!

I also encountered this problem when I used the newest DNA Master WINE build from the Baylor site. I was able to work around the issue by going back to an older version of DNA Master-WINE that I downloaded from the Baylor site last year. I updated DNA Master from within the program to the latest version, and I am able to use BLAST successfully. I'm thinking there is something wrong with the latest version of WINE itself, giving the OLE error?

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

Link to this post \| posted 14 Jan, 2016 19:36
kbutela	GregFrederick@letu.edu GregFrederick@letu.edu GregFrederick@letu.edu Kristen Butela Hi there Greg! Yes, I am currently still using WINE to run DNA Master. The great thing about WINE is that it really isn't a Windows emulator that requires a separate virtual machine-any WINE program can run on the native MacOS. From my understanding, WINE in combination with X11 provides a basic scaffold on the Mac on which Windows programs can run. All you need to do is to make sure that XQuartz/X11 (http://www.xquartz.org/) is installed on the computer (this permits WINE programs to function). Tamarah's link contains the entire DNA Master package. The Mac will treat this program as an app. Good luck, and let me know if you have any questions! Thanks Kristen. I put the "Windows Emulator" in quotes cause I had read that it's not technically an emulator. But then again they took the name from that. QUESTION: I think I have this. But I want to be certain I am correct. I am planning to give my students with Macs the link to XQuartz/X11 and a copy of Tammy's DNA-Master.dmg file. With those two pieces installed, they should be able to install, update, and run DNA Master on their OSX machines. Is this correct? Thanks again! I'm sorry for all the questions… I should play with my wife's iMac more…. I guess! Sounds to me that you do have it! All your students need to do is make sure that they have X11/XQuartz installed, and then they can download Tammy's DNA-Master.dmg file. This is all you need to run DNA Master on a Mac. Sometimes, students will have occasional issues in starting up DNA Master. Normally, when you click on DNA Master on the Mac, it automatically opens up X11. Sometimes, this doesn't happen, and DNA Master won't open (no signs are given that something is wrong). If this happens, just open up X11 on your own before starting DNA Master. I don't know why, but copying/pasting from DNA Master can stop working sometimes. To fix this, start up X11 and Navigate to X11 Preferences using the top status bar. Make sure that all boxes are checked under the Pasteboard tab. Hope this helps!

Link to this post | posted 14 Jan, 2016 19:36

kbutela

GregFrederick@letu.edu
GregFrederick@letu.edu
GregFrederick@letu.edu
Kristen Butela
Hi there Greg! Yes, I am currently still using WINE to run DNA Master. The great thing about WINE is that it really isn't a Windows emulator that requires a separate virtual machine-any WINE program can run on the native MacOS. From my understanding, WINE in combination with X11 provides a basic scaffold on the Mac on which Windows programs can run. All you need to do is to make sure that XQuartz/X11 (http://www.xquartz.org/) is installed on the computer (this permits WINE programs to function). Tamarah's link contains the entire DNA Master package. The Mac will treat this program as an app. Good luck, and let me know if you have any questions!

Thanks Kristen. I put the "Windows Emulator" in quotes cause I had read that it's not technically an emulator. But then again they took the name from that.

QUESTION: I think I have this. But I want to be certain I am correct. I am planning to give my students with Macs the link to XQuartz/X11 and a copy of Tammy's DNA-Master.dmg file. With those two pieces installed, they should be able to install, update, and run DNA Master on their OSX machines. Is this correct?

Thanks again! I'm sorry for all the questions… I should play with my wife's iMac more…. I guess!

Sounds to me that you do have it! All your students need to do is make sure that they have X11/XQuartz installed, and then they can download Tammy's DNA-Master.dmg file. This is all you need to run DNA Master on a Mac.

Sometimes, students will have occasional issues in starting up DNA Master. Normally, when you click on DNA Master on the Mac, it automatically opens up X11. Sometimes, this doesn't happen, and DNA Master won't open (no signs are given that something is wrong). If this happens, just open up X11 on your own before starting DNA Master.

I don't know why, but copying/pasting from DNA Master can stop working sometimes. To fix this, start up X11 and Navigate to X11 Preferences using the top status bar. Make sure that all boxes are checked under the Pasteboard tab.

Hope this helps!

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

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