SEA-PHAGES | All posts created by kbutela

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

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

Link to this post \| posted 13 Jan, 2016 21:29
kbutela	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!

Link to this post | posted 13 Jan, 2016 21:29

kbutela

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!

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

Link to this post \| posted 25 Sep, 2015 16:02
kbutela	Is she running the WINE bottled version of DNAMaster on a Mac? This is an issue that is easily corrected in the X11 preferences. If she's running it on a Windows machine, I'd uninstall and re-install the program. I can't recall ever having this issue on a Windows machine, but I encounter it approximately 20% of the time when my students run it on their Macbooks.

Posted in: DNA Master → Copy and paste in DNA Master

Link to this post \| posted 16 Sep, 2015 15:09
kbutela	We have been successfully using Wine to run DNA Master on the Mac for the past three years with only rare, very minor issues. The most important word of caution I have is to be careful in setting up the save preferences during initial preferences setup. The Wine program creates a "fake" windows C drive in order to properly run. The default DNA Master Archive save location is set to this "fake" C drive. I have my students create a DNA Master Archive on their Mac desktop or other readily accessible location on their Mac. When setting preferences, be sure to set the save location to this folder. Otherwise, it's nearly impossible to locate files when working on the Mac. Next, some students occasionally have difficulty cutting and pasting from DNA Master onto websites such as BLAST, HHpred, etc. This can be fixed in one of two ways: on the X11 preferences menu, make sure that you set Pasteboard settings to "Enable syncing" and all sub-options are selected. If this doesn't help, restart X11 and DNA Master. I find that sometimes the system gets overwhelmed when copying/pasting a lot of text and will stop responding to the copy paste functions. Anyone who has any specific questions about using DNA Master on the Mac can contact me for help. Although the installation seems like technology hoop jumping, once installed DNA Master will run smoothly for the majority of the time on the Mac. Edited 16 Sep, 2015 15:09

Link to this post | posted 16 Sep, 2015 15:09

kbutela

We have been successfully using Wine to run DNA Master on the Mac for the past three years with only rare, very minor issues. The most important word of caution I have is to be careful in setting up the save preferences during initial preferences setup. The Wine program creates a "fake" windows C drive in order to properly run. The default DNA Master Archive save location is set to this "fake" C drive. I have my students create a DNA Master Archive on their Mac desktop or other readily accessible location on their Mac. When setting preferences, be sure to set the save location to this folder. Otherwise, it's nearly impossible to locate files when working on the Mac.

Next, some students occasionally have difficulty cutting and pasting from DNA Master onto websites such as BLAST, HHpred, etc. This can be fixed in one of two ways: on the X11 preferences menu, make sure that you set Pasteboard settings to "Enable syncing" and all sub-options are selected. If this doesn't help, restart X11 and DNA Master. I find that sometimes the system gets overwhelmed when copying/pasting a lot of text and will stop responding to the copy paste functions.

Anyone who has any specific questions about using DNA Master on the Mac can contact me for help. Although the installation seems like technology hoop jumping, once installed DNA Master will run smoothly for the majority of the time on the Mac.

Edited 16 Sep, 2015 15:09

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

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