SEA-PHAGES | Critical Update: Installing New Copies of DNA Master or Updating Old Versions of DNA Master prior to Version 2701

Link to this post \| posted 13 Jul, 2023 20:49
kbutela	All- As of 7-13-2023, the Pitt server used to host DNA Master updates is still down due to firewall updates, and while we are making substantial progress on getting the server back online, this is an extremely complicated endeavor involving the efforts of multiple people, so we are asking for your patience while this issue is addressed. In the meantime, we have developed the following workflow for everyone to follow. If you have a functional copy of DNA Master (version 2701 or above), you do NOT need to update the program at this time. Please turn off your automatic updates by navigating to Preferences –> Timed Events and unchecking the box "Automatic checks for DNA Master updates every X days." Any "FTP Failure" error message that pops up while the server is down is more of an inconvenience at this time than anything else, and you can safely ignore them. If you need to install DNA Master on a new machine or uninstall a malfunctioning copy of DNA Master, you will need to update DNA Master using a workaround that will require you to install then manually update the program through copying and pasting files. The automatic DNA Master update would normally do this work behind the scenes for you, but because the server is down, you need to a bit of button pushing on your own. You will have a fully functional copy of DNA Master when you are finished. First, access my OneDrive folder containing the files that you will need. Please do not delete or move any of the files so that others can make use of the information. Next, download and install the "original" version of DNA Master using the dna master installer.exe file. Install normally using the instructions on PhagesDB and in the Bioinformatics Guide up until the point of updating the program. This will install the basic architecture needed to run DNA Master on your computer. Do not start DNA Master. This step is critical in the process, as the installer sets up the infrastructure needed on your computer to run DNA Master. You can't just copy my existing folder and run it on your machine; the installer must run first (believe me, I tried it.) Locate the DNA Master folder where you installed the program; have it open in a finder window. Download the "DNA Master Updated Program and Associated Files" folder from the OneDrive. This will take a few minutes and may download as a ZIP folder. Unzip the folder if needed. Copy all contents of this folder. Paste all contents from the DNA Master Updated Program and Associated Files folder into the DNA Master folder where you installed the program. You will get a series of popup windows asking if you want to merge or replace files. Hit merge when you get that option. If you only get replace, hit that option. This is the manual update process. You are now copying over all of the updated helper programs, database updates, version 2705 of DNA Master, and all associated information needed for DNA Master to properly function on your computer. After copying/replacing/merging is finished, you will notice that your DNA Master folder contains two versions of DNA Master: OldDNAMas.exe (do not use this one) and DNAMas.exe. You'll want to use DNAMas.exe. Do not delete any files or programs from the DNA Master folder. When finished, restart DNA Master. You may get a popup warning that DNA Master can't find the DMDB or Helper folders-this is normal, just redirect the program to the correct directories. Some folks get this error message when finishing the install but others do not. If you get the error-do not worry. DNA Master just needs to be pointed back to the correct location to it's DMDB database and Helper folders. You'll be prompted to those directories during the startup process. When things are back up and running, you'll see that you are now running version 2705. You can return to the setup guide and begin resetting your preferences. Be sure to turn off automatic updates while you are going through the preferences. I'm hoping that we can crowdsource any suggestions/troubleshooting tips as we work through this manual update process together, so please reply to this forum post if you have any issues or tips to share.

Link to this post | posted 13 Jul, 2023 20:49

All-

As of 7-13-2023, the Pitt server used to host DNA Master updates is still down due to firewall updates, and while we are making substantial progress on getting the server back online, this is an extremely complicated endeavor involving the efforts of multiple people, so we are asking for your patience while this issue is addressed.

In the meantime, we have developed the following workflow for everyone to follow.

If you have a functional copy of DNA Master (version 2701 or above), you do NOT need to update the program at this time. Please turn off your automatic updates by navigating to Preferences –> Timed Events and unchecking the box "Automatic checks for DNA Master updates every X days." Any "FTP Failure" error message that pops up while the server is down is more of an inconvenience at this time than anything else, and you can safely ignore them.

If you need to install DNA Master on a new machine or uninstall a malfunctioning copy of DNA Master, you will need to update DNA Master using a workaround that will require you to install then manually update the program through copying and pasting files. The automatic DNA Master update would normally do this work behind the scenes for you, but because the server is down, you need to a bit of button pushing on your own. You will have a fully functional copy of DNA Master when you are finished.

First, access my OneDrive folder containing the files that you will need. Please do not delete or move any of the files so that others can make use of the information.

Next, download and install the "original" version of DNA Master using the dna master installer.exe file. Install normally using the instructions on PhagesDB and in the Bioinformatics Guide up until the point of updating the program. This will install the basic architecture needed to run DNA Master on your computer. Do not start DNA Master. This step is critical in the process, as the installer sets up the infrastructure needed on your computer to run DNA Master. You can't just copy my existing folder and run it on your machine; the installer must run first (believe me, I tried it.)

Locate the DNA Master folder where you installed the program; have it open in a finder window.

Download the "DNA Master Updated Program and Associated Files" folder from the OneDrive. This will take a few minutes and may download as a ZIP folder. Unzip the folder if needed.

Copy all contents of this folder.

Paste all contents from the DNA Master Updated Program and Associated Files folder into the DNA Master folder where you installed the program. You will get a series of popup windows asking if you want to merge or replace files. Hit merge when you get that option. If you only get replace, hit that option. This is the manual update process. You are now copying over all of the updated helper programs, database updates, version 2705 of DNA Master, and all associated information needed for DNA Master to properly function on your computer.

After copying/replacing/merging is finished, you will notice that your DNA Master folder contains two versions of DNA Master: OldDNAMas.exe (do not use this one) and DNAMas.exe. You'll want to use DNAMas.exe. Do not delete any files or programs from the DNA Master folder.

When finished, restart DNA Master. You may get a popup warning that DNA Master can't find the DMDB or Helper folders-this is normal, just redirect the program to the correct directories. Some folks get this error message when finishing the install but others do not. If you get the error-do not worry. DNA Master just needs to be pointed back to the correct location to it's DMDB database and Helper folders. You'll be prompted to those directories during the startup process.

When things are back up and running, you'll see that you are now running version 2705. You can return to the setup guide and begin resetting your preferences. Be sure to turn off automatic updates while you are going through the preferences.

I'm hoping that we can crowdsource any suggestions/troubleshooting tips as we work through this manual update process together, so please reply to this forum post if you have any issues or tips to share.

Link to this post \| posted 01 Aug, 2023 19:46
mespariz	Hi Kristen, I followed your steps and successfully obtained an updated version of DNA Master. However, I'm facing an issue when trying to open a previously saved dnam5 file. I'm receiving a "Database Failure" message, which is causing all the dnam5 files to appear empty. It seems like there might be a problem with the database. Could you please assist me in resolving this issue? Your help would be greatly appreciated. Thank you, Martín

Link to this post | posted 01 Aug, 2023 19:46

mespariz

Hi Kristen,

I followed your steps and successfully obtained an updated version of DNA Master. However, I'm facing an issue when trying to open a previously saved dnam5 file. I'm receiving a "Database Failure" message, which is causing all the dnam5 files to appear empty. It seems like there might be a problem with the database. Could you please assist me in resolving this issue? Your help would be greatly appreciated.

Thank you,
Martín

Link to this post \| posted 03 Aug, 2023 16:31
kbutela	Hi Martin- I have a few suggestions to help you troubleshoot your install. Before proceeding, make sure you are running DNA Master as an administrator. For some installations, DNA Master temporarily loses it's connection to the DMDB database folder, and it just needs to be relocated. To do this, check your preferences –> Local settings –> Directories. Look for the location of the Databases. It should point to wherever directory you saved DNA Master, something like C:\Program Files\DNA Master\DMDB\. Regardless of what it says, click on the "Browse" button and locate the DMDB folder in your DNA Master directory. This will tell DNA Master where the databases are and reset the connection. While you are in the Directories panel, it's probably a good idea to check all of your local settings to make sure they are correct. Click "Apply" to update your changes and "Ok." You can then close the preferences window. Exit and restart DNA Master, and then attempt to reopen your file. If this does not work, try to open a different dnam5 file. If you cannot open any files with DNA Master after resetting the location of your databases, then try uninstalling DNA Master and reinstalling the program using the instructions provided in this post. Because you are manually updating the program, make sure you move slowly through the "replace" and "merge" prompts. During my initial testing of this method, I found that one missed prompt can corrupt the installation process because files can get skipped. When you start the reinstalled program as an administrator, I'd again recommend double checking preferences again to make sure the correct directories are set. I had to reset my databases and helper program directories when I used this method, but some others don't. Hope this helps! mespariz Hi Kristen, I followed your steps and successfully obtained an updated version of DNA Master. However, I'm facing an issue when trying to open a previously saved dnam5 file. I'm receiving a "Database Failure" message, which is causing all the dnam5 files to appear empty. It seems like there might be a problem with the database. Could you please assist me in resolving this issue? Your help would be greatly appreciated. Thank you, Martín

Link to this post | posted 03 Aug, 2023 16:31

kbutela

Hi Martin-

I have a few suggestions to help you troubleshoot your install. Before proceeding, make sure you are running DNA Master as an administrator.

For some installations, DNA Master temporarily loses it's connection to the DMDB database folder, and it just needs to be relocated. To do this, check your preferences –> Local settings –> Directories. Look for the location of the Databases. It should point to wherever directory you saved DNA Master, something like C:\Program Files\DNA Master\DMDB\. Regardless of what it says, click on the "Browse" button and locate the DMDB folder in your DNA Master directory. This will tell DNA Master where the databases are and reset the connection. While you are in the Directories panel, it's probably a good idea to check all of your local settings to make sure they are correct. Click "Apply" to update your changes and "Ok." You can then close the preferences window. Exit and restart DNA Master, and then attempt to reopen your file.

If this does not work, try to open a different dnam5 file. If you cannot open any files with DNA Master after resetting the location of your databases, then try uninstalling DNA Master and reinstalling the program using the instructions provided in this post. Because you are manually updating the program, make sure you move slowly through the "replace" and "merge" prompts. During my initial testing of this method, I found that one missed prompt can corrupt the installation process because files can get skipped.

When you start the reinstalled program as an administrator, I'd again recommend double checking preferences again to make sure the correct directories are set. I had to reset my databases and helper program directories when I used this method, but some others don't. Hope this helps!

mespariz
Hi Kristen,

I followed your steps and successfully obtained an updated version of DNA Master. However, I'm facing an issue when trying to open a previously saved dnam5 file. I'm receiving a "Database Failure" message, which is causing all the dnam5 files to appear empty. It seems like there might be a problem with the database. Could you please assist me in resolving this issue? Your help would be greatly appreciated.

Thank you,
Martín

Link to this post \| posted 02 Jan, 2024 22:12
kbutela	The DNA Master update server is back online as of 1/2/2024, so there is no need to perform the workaround solution on this page.

Link to this post \| posted 06 Mar, 2024 23:14
sheninger	Is the server down again? We have been having problems running DNA Master since Feb 29th. get update error. the whole thing freezes as its trying to connect to home site.

Link to this post \| posted 07 Mar, 2024 15:51
crump.katie	Hi everyone- I have the same question as sheninger. Unfortunately, DNA Master was erased from our school computers over Spring Break. Our IT tried to re-install it. They are running into the following problems: 1) DNA Master will not update because it says FTP Failure 2) We cannot bypass the FTP failure issue as described in the installation guide because we are missing some of the tabs in the preferences 3) Our IT cannot download using the workaround described by Kristen above because our institution won't let us download from a One Drive folder Can anyone please advise? Thanks! Katie

Link to this post | posted 07 Mar, 2024 15:51

crump.katie

Hi everyone-

I have the same question as sheninger.

Unfortunately, DNA Master was erased from our school computers over Spring Break. Our IT tried to re-install it. They are running into the following problems:

1) DNA Master will not update because it says FTP Failure
2) We cannot bypass the FTP failure issue as described in the installation guide because we are missing some of the tabs in the preferences
3) Our IT cannot download using the workaround described by Kristen above because our institution won't let us download from a One Drive folder

Can anyone please advise?

Thanks!
Katie

Link to this post \| posted 07 Mar, 2024 15:58
debbie	Hi Katie and Steve, The space where the DNA Master server lives is undergoing renovations. It is expected to be back next week. I'll keep you posted. debbie Edited 07 Mar, 2024 16:07

Link to this post \| posted 12 Mar, 2024 16:02
crump.katie	Hi Debbie, Thanks for the response. Has there been any updates on the completion of the renovations of DNA Master? We still can't get it to update without the FTP failure notice. Thanks, Katie

Link to this post \| posted 14 Mar, 2024 15:35
kbutela	Hi Katie- Do you know what folders your university will enable you to download from, like Dropbox or Google Drive? Thanks, Kristen

Link to this post \| posted 22 Mar, 2024 16:55
debbie	debbie Hi Katie and Steve, The space where the DNA Master server lives is undergoing renovations. It is expected to be back next week. I'll keep you posted. debbie DNA Master's website is back up! 3/22/24 best, debbie

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Critical Update: Installing New Copies of DNA Master or Updating Old Versions of DNA Master prior to Version 2701