Link to this post | posted 04 Aug, 2016 03:58

cdshaffer

A new beta version of Starterator has been posted. If you are running the current Beta version you should recieve an automatic update the next time you start up Starterator. If the update succeeds you will see the new version 1.1.1 in the title of the Starterator window. If you are not running the beta version and would like to install it, see the beta release post in this Starterator forum. This version has several updates and improvements: 1. New updated protocol for grouping genes into a single track. Some visually identical genes that were not being properly grouped. 2. Changes to individual track graphics: a. Change number of labels from 5 to 1 b. Annotation starts differ by color: yellow are auto-annotations (i.e. draft quality); green are starts published in GenBank 3. Change error message to recommend checking the Starterator Troubleshooting guide in seaphages forum when getting crashes 4. Whole genome analysis now creates a text file for PECAAN so you don't need to copy/paste out of the PDF. I have done limited testing on this but it appears to work (feedback appreciated if it does not work for you). You will find the text file in the "Intermediate Files" directory found inside the .starterator folder (see item 2 of the troubleshooting post in this forum if you don't know how to get to that folder), the file name will start with the name of the phage and end with "SuggestedStarts.txt". 5. Many minor bug fixes Thanks to everyone for all the beta testing and feedback, please do continue to get in touch with any and all problems or ideas for improvements.

Link to this post | posted 04 Aug, 2016 05:37
jparker	Hi Chris, My Startator beta does not seem to be automatically downloading the 1.1.1 automatic update. Is there a force update option? Thanks, Jordan

Link to this post | posted 04 Aug, 2016 16:23

cdshaffer

Hmmm It's possible I didn't set things up correctly so I we need to "divide and conquer". The first step is a good network connection, it could be that the VM cannot get to the internet to download. Can you see if your VM can connect to the internet? You can check that easily by opening a browser and seeing if you can load seaphages.org from inside the SEA virtual machine. If that works then your network is up and running so start up Starterator again and see if the update to v1.1.1 works. I know my VM often loses network connection (I am using VirtualBox), for me a simple reboot of the VM usually fixes the network, if you have confirmed that the network is up and running and the update still fails, post another message here and we can proceed to the next step. Edited 04 Aug, 2016 16:25

Link to this post | posted 05 Aug, 2016 00:20
lhughes	Chris: Just tried it on my machine as well. It stayed on version 1.1.0 and I definitely had internet connectivity in the Virtual Box. Even opened, closed and then reopened Starterator Beta to see if there was any change. Lee

Link to this post | posted 05 Aug, 2016 01:07

cdshaffer

OK I probably set up something incorrectly. I think the next thing to try is just reinstall the beta version following the same instructions. I posted the link to the pdf in the other discussion thread but briefly (assuming you did not delete any files) open terminal and enter this command: cd ~/Downloads then enter this command: bash installBetaStarterator.sh let me know if that works of fails, that worked on my version of the SEA2016 VM

Link to this post | posted 05 Aug, 2016 01:08
jparker	I tried the things that Lee tried, as well. Had connectivity and restarted the VM. I use VMware Fusion, though. Does that make a difference? Jordan

Link to this post | posted 05 Aug, 2016 01:39
jparker	Reinstalling the beta version worked. Thanks Chris!