SEA-PHAGES | Running DNA Master on a Mac using Wine

Link to this post \| posted 26 Apr, 2017 22:42
Tamarah_Adair	OK. I'm going to try it again tonight on another non-campus computer. https://baylor.box.com/s/d359kqad4rktrue2olj0sc6toa74csvy Here is a link to the DNAMAster file. I just tried to BLAST gene 1 and I got an OLE error. Thanks, Tammy

Link to this post \| posted 26 Apr, 2017 23:41
kwhutch	Tammy, I've yet to find a solution when I get an OLE error so I routinely do a re-install. And I start from scratch (and I just noticed there was a posting in February asking about how I clean out the old stuff first). First step is to make sure all your dnam5 files are backed up. And I follow Kristen's suggestion from a year ago and set up DNA Master so that the Archives are in a folder that is easily accessible such as a subfolder in Documents. Maybe there is a more efficient way and maybe you already know this…but: Open up a Terminal Window. You should see: Your-Computer-Name: ~ yourname$ Type in: cd Library/Application\ Support (cd = change directory) and hit Enter Type in: ls (ls = list) and hit Enter You'll see a long list of file and directory names. All you need to worry about are two. In the list you should see: Wine …. and edu.baylor.sts.dnamater_145451243632104 (or some other long number) Type in: rm -r Wine (rm = remove, the -r switch tells it to remove recursively, in other words all the files as subdirectories) Type in: rm - r edu.baylor.sts.dnamater_145451243632104 (or whatever number you see) and hit Enter NOTE: a short cut in Terminal is autofill. Type rm -r edu.baylor and hit Tab and it will fill in the rest. At this point you can close the terminal window and re-install DNA Master from the DMG file. I have sometimes gotten away with just doing the reinstall as has an occasional student. But it has failed often enough that I clean it all out as start again. The only thing saved is as I noted above, my dnam5 files. And that's done in advance as the above could delete them as well. Hope that helps, Keith Edited 26 Apr, 2017 23:43

Link to this post | posted 26 Apr, 2017 23:41

kwhutch

Tammy,

I've yet to find a solution when I get an OLE error so I routinely do a re-install. And I start from scratch (and I just noticed there was a posting in February asking about how I clean out the old stuff first). First step is to make sure all your dnam5 files are backed up. And I follow Kristen's suggestion from a year ago and set up DNA Master so that the Archives are in a folder that is easily accessible such as a subfolder in Documents.

Maybe there is a more efficient way and maybe you already know this…but:
Open up a Terminal Window.
You should see:
Your-Computer-Name: ~ yourname$
Type in: cd Library/Application\ Support (cd = change directory)
and hit Enter
Type in: ls (ls = list)
and hit Enter
You'll see a long list of file and directory names. All you need to worry about are two.
In the list you should see:
Wine
…. and
edu.baylor.sts.dnamater_145451243632104 (or some other long number)
Type in:
rm -r Wine (rm = remove, the -r switch tells it to remove recursively, in other words all the files as subdirectories)

Type in: rm - r edu.baylor.sts.dnamater_145451243632104 (or whatever number you see)
and hit Enter
NOTE: a short cut in Terminal is autofill. Type rm -r edu.baylor and hit Tab and it will fill in the rest.

At this point you can close the terminal window and re-install DNA Master from the DMG file. I have sometimes gotten away with just doing the reinstall as has an occasional student. But it has failed often enough that I clean it all out as start again. The only thing saved is as I noted above, my dnam5 files. And that's done in advance as the above could delete them as well.

Hope that helps,
Keith

Edited 26 Apr, 2017 23:43

Link to this post \| posted 27 Apr, 2017 16:14
cdshaffer	As much as I love the command line (and I do really), if you want to use the finder to delete everything: 1. select the finder 2. Hold down the Option Key while you select the GO menu 3. Select Library to open a finder window of your Library folder 4. Double click to open "Application Support" folder 5. Drag the Wine and edu.baylor… folders to the trash 6. Proceed with re-installation Also, I just tried a BLAST search with a fresh wine bottle install (and update of DNA Master) and I too got the OLE error. Tried on my windows virtualbox and BLAST worked just fine.

Link to this post | posted 27 Apr, 2017 16:14

cdshaffer

As much as I love the command line (and I do really), if you want to use the finder to delete everything:

1. select the finder
2. Hold down the Option Key while you select the GO menu
3. Select Library to open a finder window of your Library folder
4. Double click to open "Application Support" folder
5. Drag the Wine and edu.baylor… folders to the trash
6. Proceed with re-installation

Also, I just tried a BLAST search with a fresh wine bottle install (and update of DNA Master) and I too got the OLE error. Tried on my windows virtualbox and BLAST worked just fine.

Link to this post \| posted 28 Apr, 2017 00:05
Tamarah_Adair	Thank you Keith and Chris. I feel like my students. I waited until the due date and now I have technical problems!

Link to this post \| posted 28 Apr, 2017 00:19
kwhutch	Tamarah Adair Thank you Keith and Chris. I feel like my students. I waited until the due date and now I have technical problems! I liked Chris' info. Didn't know that about that as a way to find hidden files on a Mac. The other time I get an OLE error is the XQuartz version doesn't match up well with OS version and possibly the machine. I've a new Mac running Sierra and that works with XQuartz 2.7.11. But my older machine, running Yosemite, has problems with anything newer than 2.7.7. It seems like that should be a one time fix but it hasn't always been so. Keith

Link to this post | posted 28 Apr, 2017 00:19

kwhutch

Tamarah Adair
Thank you Keith and Chris. I feel like my students. I waited until the due date and now I have technical problems!

I liked Chris' info. Didn't know that about that as a way to find hidden files on a Mac.

The other time I get an OLE error is the XQuartz version doesn't match up well with OS version and possibly the machine. I've a new Mac running Sierra and that works with XQuartz 2.7.11. But my older machine, running Yosemite, has problems with anything newer than 2.7.7. It seems like that should be a one time fix but it hasn't always been so.

Keith

Link to this post \| posted 07 Jun, 2017 18:33
kurt.regner@unlv.edu	Hello: Thanks, this was very helpful. I installed DNA Master for Mac yesterday and everything seems to work fine. I'll post any questions. Kurt Regner, UNLV Edited 08 Jun, 2017 18:58

Link to this post \| posted 21 Dec, 2017 16:45
MSMC	I have a non-installation question about DNA Master WINE. We're going to try to use the WINE version this year; last year my IT department tried to use a network-based virtual interface so students didn't have to install a virtual machine and windows, and it was not very successful. I can run WINE on my Mac (Yosemite), but how do people resize the gene list in the features window? I cannot seem to right-click using my MacBook Air trackpad, has anyone found a workaround?

Link to this post | posted 21 Dec, 2017 16:45

MSMC

I have a non-installation question about DNA Master WINE. We're going to try to use the WINE version this year; last year my IT department tried to use a network-based virtual interface so students didn't have to install a virtual machine and windows, and it was not very successful. I can run WINE on my Mac (Yosemite), but how do people resize the gene list in the features window? I cannot seem to right-click using my MacBook Air trackpad, has anyone found a workaround?

Link to this post \| posted 22 Dec, 2017 03:46
kklyczek	Evan Merkhofer I have a non-installation question about DNA Master WINE. We're going to try to use the WINE version this year; last year my IT department tried to use a network-based virtual interface so students didn't have to install a virtual machine and windows, and it was not very successful. I can run WINE on my Mac (Yosemite), but how do people resize the gene list in the features window? I cannot seem to right-click using my MacBook Air trackpad, has anyone found a workaround? Hi Evan, This issue came up for a few folks at the bioinformatics workshop. What seemed to work is to change the settings in System Preferences > Trackpad to turn on the two-finger "secondary" click (see screen shot attached) - that appears to be the equivalent of a right click. Karen

Link to this post | posted 22 Dec, 2017 03:46

kklyczek

Evan Merkhofer
I have a non-installation question about DNA Master WINE. We're going to try to use the WINE version this year; last year my IT department tried to use a network-based virtual interface so students didn't have to install a virtual machine and windows, and it was not very successful. I can run WINE on my Mac (Yosemite), but how do people resize the gene list in the features window? I cannot seem to right-click using my MacBook Air trackpad, has anyone found a workaround?

Hi Evan,

This issue came up for a few folks at the bioinformatics workshop. What seemed to work is to change the settings in System Preferences > Trackpad to turn on the two-finger "secondary" click (see screen shot attached) - that appears to be the equivalent of a right click.

Karen

Link to this post \| posted 27 Dec, 2017 15:08
MSMC	Karen Klyczek Evan Merkhofer I have a non-installation question about DNA Master WINE. We're going to try to use the WINE version this year; last year my IT department tried to use a network-based virtual interface so students didn't have to install a virtual machine and windows, and it was not very successful. I can run WINE on my Mac (Yosemite), but how do people resize the gene list in the features window? I cannot seem to right-click using my MacBook Air trackpad, has anyone found a workaround? Hi Evan, This issue came up for a few folks at the bioinformatics workshop. What seemed to work is to change the settings in System Preferences > Trackpad to turn on the two-finger "secondary" click (see screen shot attached) - that appears to be the equivalent of a right click. Karen Thanks so much Karen! I'm going to give this a go, WINE should save us some headaches this year. Happy New Years everyone! Evan

Link to this post | posted 27 Dec, 2017 15:08

MSMC

Karen Klyczek
Evan Merkhofer
I have a non-installation question about DNA Master WINE. We're going to try to use the WINE version this year; last year my IT department tried to use a network-based virtual interface so students didn't have to install a virtual machine and windows, and it was not very successful. I can run WINE on my Mac (Yosemite), but how do people resize the gene list in the features window? I cannot seem to right-click using my MacBook Air trackpad, has anyone found a workaround?

Hi Evan,

This issue came up for a few folks at the bioinformatics workshop. What seemed to work is to change the settings in System Preferences > Trackpad to turn on the two-finger "secondary" click (see screen shot attached) - that appears to be the equivalent of a right click.

Karen

Thanks so much Karen! I'm going to give this a go, WINE should save us some headaches this year. Happy New Years everyone!

Evan

Link to this post \| posted 11 Jan, 2018 18:33
delesall	Hi all I just downloaded DNAMaster from the Baylor site (https://baylor.app.box.com/v/DNAMasterMac) using the version from 2017.5.23 I have been able to upload a sequence but when I do an auto-annotation (no blasting) nothing appears in the features? Any advice? And has somebody compiled a document on issues and things to know about running DNAMaster on a mac and is willing to share? Thanks and happy annotating in 2018! Veronique

Link to this post | posted 11 Jan, 2018 18:33

delesall

Hi all

I just downloaded DNAMaster from the Baylor site (https://baylor.app.box.com/v/DNAMasterMac) using the version from 2017.5.23

I have been able to upload a sequence but when I do an auto-annotation (no blasting) nothing appears in the features? Any advice?

And has somebody compiled a document on issues and things to know about running DNAMaster on a mac and is willing to share?

Thanks and happy annotating in 2018! Veronique

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Running DNA Master on a Mac using Wine