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

Link to this post \| posted 04 Feb, 2016 20:56
kwhutch	Dan Russell Tamarah Adair Yesterday we tried this new version out in lab and I was able to BLAST. The newest version to the box account is at the following link: https://baylor.box.com/s/sct7ixend1d29cn5n7qjlbcfod98hyny Changes: Rebuilt wine bottler package based on wine bottler 1.8rc4 (needed for El Capitan support) Updated to current version of DNAMaster (5.22.23 dated 1/26/16) Awesome, Tammy. Thanks for doing this. Hopefully this new version will work for everyone. –Dan Thanks to both Tammy and to Kristen. Both solutions work. Tammy's new dmg works and installing DNA Master in the virtual machine works. Which also tells me I can get DNA Master working on my non-virtual Linux machines. Keith

Link to this post | posted 04 Feb, 2016 20:56

Dan Russell
Tamarah Adair
Yesterday we tried this new version out in lab and I was able to BLAST. The newest version to the box account is at the following link:

https://baylor.box.com/s/sct7ixend1d29cn5n7qjlbcfod98hyny
Changes:
Rebuilt wine bottler package based on wine bottler 1.8rc4 (needed for El Capitan support)
Updated to current version of DNAMaster (5.22.23 dated 1/26/16)

Awesome, Tammy. Thanks for doing this. Hopefully this new version will work for everyone.

–Dan

Thanks to both Tammy and to Kristen. Both solutions work. Tammy's new dmg works and installing DNA Master in the virtual machine works. Which also tells me I can get DNA Master working on my non-virtual Linux machines.

Keith

Link to this post \| posted 04 Feb, 2016 21:06
Tamarah_Adair	I just did a BLAST all genes on KylieMac and received the results in 15 minutes- in the Features BLAST window! Oh Happy Day!

Link to this post \| posted 05 Feb, 2016 03:55
kwhutch	Tamarah Adair I just did a BLAST all genes on KylieMac and received the results in 15 minutes- in the Features BLAST window! Oh Happy Day! I was happy too after first installing and doing an initial run, auto-annotating and a low level of BLASTing (you must have a local server for BLAST. NCBI never treats our submissions so kindly). Anyhow after doing some other work and getting back to running it tonight to finish a BLAST the performance has degraded. The major problem is that the dropdown menus often are blank. But sometimes the whole things freezes. I know it runs slow but this was much slower. What version of XQuartz are you using? It really is something that is controlling window behavior that goes wrong. Is there an X11 app that gets installed with WINE that maybe gets over-written by XQuartz? Grasping at straws here as to why the fairly rapid loss of function.

Link to this post | posted 05 Feb, 2016 03:55

kwhutch

Tamarah Adair
I just did a BLAST all genes on KylieMac and received the results in 15 minutes- in the Features BLAST window! Oh Happy Day!

I was happy too after first installing and doing an initial run, auto-annotating and a low level of BLASTing (you must have a local server for BLAST. NCBI never treats our submissions so kindly).

Anyhow after doing some other work and getting back to running it tonight to finish a BLAST the performance has degraded. The major problem is that the dropdown menus often are blank. But sometimes the whole things freezes. I know it runs slow but this was much slower.

What version of XQuartz are you using? It really is something that is controlling window behavior that goes wrong. Is there an X11 app that gets installed with WINE that maybe gets over-written by XQuartz? Grasping at straws here as to why the fairly rapid loss of function.

Link to this post \| posted 05 Feb, 2016 12:06
kwhutch	Keith Hutchison Tamarah Adair I just did a BLAST all genes on KylieMac and received the results in 15 minutes- in the Features BLAST window! Oh Happy Day! I was happy too after first installing and doing an initial run, auto-annotating and a low level of BLASTing (you must have a local server for BLAST. NCBI never treats our submissions so kindly). Anyhow after doing some other work and getting back to running it tonight to finish a BLAST the performance has degraded. The major problem is that the dropdown menus often are blank. But sometimes the whole things freezes. I know it runs slow but this was much slower. What version of XQuartz are you using? It really is something that is controlling window behavior that goes wrong. Is there an X11 app that gets installed with WINE that maybe gets over-written by XQuartz? Grasping at straws here as to why the fairly rapid loss of function. Solved it with regard to getting it working again. It required going back to IQuartz2.7.5. The point really is that there is a IQuartz/X11 component to this set of problems.

Link to this post | posted 05 Feb, 2016 12:06

kwhutch

Keith Hutchison
Tamarah Adair
I just did a BLAST all genes on KylieMac and received the results in 15 minutes- in the Features BLAST window! Oh Happy Day!

I was happy too after first installing and doing an initial run, auto-annotating and a low level of BLASTing (you must have a local server for BLAST. NCBI never treats our submissions so kindly).

Anyhow after doing some other work and getting back to running it tonight to finish a BLAST the performance has degraded. The major problem is that the dropdown menus often are blank. But sometimes the whole things freezes. I know it runs slow but this was much slower.

What version of XQuartz are you using? It really is something that is controlling window behavior that goes wrong. Is there an X11 app that gets installed with WINE that maybe gets over-written by XQuartz? Grasping at straws here as to why the fairly rapid loss of function.

Solved it with regard to getting it working again. It required going back to IQuartz2.7.5. The point really is that there is a IQuartz/X11 component to this set of problems.

Link to this post \| posted 28 Jan, 2017 20:45
ball.1766	Most of our students this year are using Macs so they are trying to run DNA Master using WINE but we are running into issues. None of them seem to be able to run the auto-annotation or BLAST genes (individual or batch) and a few of them cannot even open a .dnam5 file that I provided as a work around (I ran the auto-annotation and BLAST and just distributed the file). Any suggestions? I'm a PC person so I don't have the slightest idea of where to start troubleshooting.

Link to this post | posted 28 Jan, 2017 20:45

ball.1766

Most of our students this year are using Macs so they are trying to run DNA Master using WINE but we are running into issues. None of them seem to be able to run the auto-annotation or BLAST genes (individual or batch) and a few of them cannot even open a .dnam5 file that I provided as a work around (I ran the auto-annotation and BLAST and just distributed the file). Any suggestions? I'm a PC person so I don't have the slightest idea of where to start troubleshooting.

Link to this post \| posted 28 Jan, 2017 22:15
kbutela	I know there were some similar problems with the pre-2016 box file hosted at Baylor, but Tammy was able to get them to upload a version that worked, which is the current dmg file hosted on the Baylor Box site. Are they getting particular error messages? What exactly is happening when they attempt to open the file? Have they performed the update to the secure BLAST servers (some of my students forgot this step)?

Link to this post | posted 28 Jan, 2017 22:15

kbutela

I know there were some similar problems with the pre-2016 box file hosted at Baylor, but Tammy was able to get them to upload a version that worked, which is the current dmg file hosted on the Baylor Box site. Are they getting particular error messages? What exactly is happening when they attempt to open the file? Have they performed the update to the secure BLAST servers (some of my students forgot this step)?

Link to this post \| posted 29 Jan, 2017 04:36
kwhutch	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.

Link to this post | posted 29 Jan, 2017 04:36

kwhutch

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.

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.

Link to this post \| posted 26 Apr, 2017 22:09
Tamarah_Adair	Is anyone else having issues BLASTing in DNAMaster/Wine? I have not been able to get any BLAST results for 3 days. Either I get an OLE error or the BLAST fails or hangs up. I have tried single genes, entire genomes, and several different files. I don't think anything has changed on my end, so I'm wondering if NCBI made any changes?

Link to this post \| posted 26 Apr, 2017 22:29
kbutela	I've been BLASTing just fine over the last few days. My DNA Master version is 5.23.1, build 2492, 29 January 2017. A lot of people, including myself, seemed to have trouble earlier in the semester, and I seem to recall that the group conclusion (maybe on another post?) was that the NCBI servers were getting too many simultaneous requests from the same place/school, so Blast was kicking people out, resulting in DNA Master throwing the error.

Link to this post | posted 26 Apr, 2017 22:29

kbutela

I've been BLASTing just fine over the last few days. My DNA Master version is 5.23.1, build 2492, 29 January 2017. A lot of people, including myself, seemed to have trouble earlier in the semester, and I seem to recall that the group conclusion (maybe on another post?) was that the NCBI servers were getting too many simultaneous requests from the same place/school, so Blast was kicking people out, resulting in DNA Master throwing the error.

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Running DNA Master on a Mac using Wine