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All posts created by chg60

| posted 01 Feb, 2022 01:35
I can install VirtualBox, but then need to choose between the Mac or Windows VM download.

Can you please attach an image to illustrate what you mean by this? I have successfully run the SEA VM on several flavors of Linux, including Linux Mint, so I should be able to help once I properly understand the problem!
Posted in: SEA-PHAGES Virtual MachineInstalling SEA VM on Linux machine
| posted 27 Jul, 2021 18:56
One solution which at least used to work (I have not verified recently), is to download and install Bitvise SSH Client. Assuming nothing has changed with this approach, once installation completes the SSL libraries will now be in place for other programs (e.g. DNA Master) to use.
Posted in: DNA MasterSSL error
| posted 30 Jun, 2021 19:51

Should contain the 2017 SEA_VM, 2020 SEA_VM, and the video + bashrc file to get the 2020 SEA_VM file checker working again.
Posted in: SEA-PHAGES Virtual MachineFresh Install = no Validation folder
| posted 28 Jun, 2021 16:10
Hi Steve,

Did you download a 2017 SEA_VM or the 2020 SEA_VM?

In either case, you can simply create a folder called "validation" in the home directory (default location when you launch a new file browser instance).

In the validation folder, you should create another folder called "genomes"; also copy in to the validation folder the new config.txt and a copy of import_table.csv you may have lying around.

All other steps in the video should work, unless you have a fresh copy of a VERY old VM.
Posted in: SEA-PHAGES Virtual MachineFresh Install = no Validation folder
| posted 28 Jun, 2021 14:33
Ugh - Sorry Kristen, Claire Rinehart pointed that one out to me already and I forgot to update the document to reflect that.

I'd be grateful for your annotated version when you're done.
Posted in: Notes and Final FilesNew File Checker for Mac
| posted 26 Jun, 2021 16:43
Hi Kristen,

Sorry the ReadTheDocs instructions don't seem to be working for you. I'll spend some time reviewing those and hopefully get it straightened out. Would be helpful to hear from you if there are steps in particular not working.

In the meantime, would you mind trying to use the instructions and resources found in the attached .zip file? Instructions are still a work in progress so if anything still needs to be clarified please let me know!


Posted in: Notes and Final FilesNew File Checker for Mac
| posted 19 Feb, 2021 12:42
Glad to have been able to help, though it sounds like you did most of the heavy lifting!

This is an alternative way of accomplishing the fresh 'installation' of PhamNexus that you did manually (won't be much help for you anymore, but hopefully will help anyone else that ends up here!). In a terminal inside the SEA_VM:

cd ~/
rm -r phamnexus
git clone

The first steps will make sure you're in the home directory, and delete the existing 'phamnexus' directory. The last step will download the repository and put it in a new folder called 'phamnexus', as opposed to the '~/Downloads/phamnexus-master' folder that happens if you download from GitHub in a web browser and then unzip.

I suspect that downloading the latest Actino_Draft.sql file from had little impact unless you also executed a command like:

mysql -u root -p Actino_Draft < /path/to/Actino_Draft.sql

This command (or a host of similar ones) would overwrite the existing Actino_Draft database with the database contained in your Actino_Draft.sql, and is exactly what PhamNexus does behind the scenes when it successfully performs database updates.
Posted in: Bioinformatic Tools and AnalysesPhamNexus on SEA-VM
| posted 17 Feb, 2021 17:55

Thanks (again) Chris for alerting me to this post! At the end of last year we changed where the databases are hosted, and then I failed to update the URL in PhamNexus. I've now made the relevant changes, and at least on my local computer it appears as though the new version works.

In your SEA_VM, launch PhamNexus, then click Help > Check for Updates. It should notice that there are updates available, and prompt you to allow it to download. Once it finishes, restart PhamNexus and you should now be able to get database updates again. Assuming you've not updated the database within the last week, there should be a new database available.

The database download/update process can take a few minutes, depending on your internet speed and computer hardware. The fastest I've seen it is on my dev machine, about 15 seconds.

Hopefully, that's all there is to it! Please post a reply whatever the outcome, so I'll know whether there's additional work for me to do!
Posted in: Bioinformatic Tools and AnalysesPhamNexus on SEA-VM
| posted 25 Jan, 2021 18:04
Hi Tammy,

The short answer with respect to the lack of 32-bit support on macOS Mojave/Catalina/Big Sur, and the Apple silicon Macs, is that there's still a good deal of uncertainty.

As you mentioned, for now, Wine does not work on Catalina, but the parent company (CodeWeavers) offers a paid tool (CrossOver) that works on Catalina (on Intel Macs) and Big Sur (on Apple silicon) and is documented as running 32-bit programs with no obvious degradation of performance. It's $40 so it's not a great option, but if it works it is at least an option. There is also a good chance that at some point this functionality makes its way into Wine, but I can't say with any certainty how soon that would happen.

Virtualization tools like Parallels, VMWare, and VirtualBox should all allow DNA Master to work on Mojave or Catalina on Intel Macs, and will probably also soon work on Big Sur. The Apple Silicon question is a big one here - none of these companies have yet made any kind of commitments about what they will or won't do. All seem to be working on something for Apple silicon but to my knowledge there are no details about which operating systems or capabilities will be supported.

All this to say - for everything except the Apple silicon Macs, there are solutions either known to work or likely to work. For the new Macs, we'll have to wait and see.

Posted in: Using WINE to run DNA Master on a MacLink to Baylor box