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Recent Activity
All posts created by cdshaffer
Link to this post | posted 21 Sep, 2016 00:25 | |
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Jordan, Just in case you are working on phage while you try to fix your VM. There was just a new phamerator database release so I created an updated set of pham reports for this more recent version. You can download the new complete set of starterator pham reports from this url: https://wustl.box.com/v/Starterator73 |
Posted in: Starterator → Starterator completely bricked
Link to this post | posted 20 Sep, 2016 14:41 | |
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OH foo, there was a typo in that command, should the Applications not Application in that line, sorry about that. I should not have tried to write that from memory. Can you try again with this command in the seastudent account and copy/paste back the results: /home/seastudent/Applications/Starterator/starterator/starterator.sh In the mean time I think this might help for the seafaculty account: Try to do a reinstall of the beta version but modify these commands instead of add this "–fix-missing" to the command so it looks like this: this fixes some weirdness due to google chrome which breaks that upgrade command.Continue with the instructions, then after you run the installer script with the command:
You need to copy one file, so use the file browser and in your home folder and go through the following folders Applications -> Starterator -> starterator -> starterator -> extras in that folder should be a file called starterator.svg. Click once on that file to select it, then go to the magic appearing edit menu at the top and select copy. Then navigate back to your home folder and open the .starterator folder. The use that same edit menu and select paste. You should see a copy of the starterator.svg file appear. Now try running starterator. Let me know how things go or if you get stuck. |
Posted in: Starterator → Starterator completely bricked
Link to this post | posted 19 Sep, 2016 16:40 | |
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Jordan, Sorry for the late reply, I was traveling all weekend. I don't know how but something is corrupting both the student version and the beta version is the faculty account. Those two should be completely independent so I need more info. Can you login to the student account and open the terminal and type this: /home/seastudent/Applications/Starterator/starterator/starterator.sh a bunch of text should show up on the screen. let me know if that works and starterator starts up. If you still get the error, scroll back, and try to copy all of what the computer printed in the terminal and paste it in another message below. While we are working this out, if you want to continue working on your phage, you can download the complete collection of starterator reports from this link: https://wustl.box.com/v/Starterator72 that is a compressed zip archive of all starterator reports organized by pham. It is based on the most recent version 72 of the phamerator database. Just download, double click and you should get a folder with all the reports. You will need the pham number for your gene of interest which you can get from phagesdb |
Posted in: Starterator → Starterator completely bricked
Link to this post | posted 01 Sep, 2016 17:36 | |
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OK I will look into this, see if I can replicate the issue. |
Link to this post | posted 12 Aug, 2016 17:21 | |
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The next round of udpates to Starterator will be with the various text output sections. I am seeking input from the user community on what improvements they would like to see in the output. Please feel free to post to the forum on any or all of the following: Is there any text output that you find confusing? Can you suggest better wording? Is there anything missing from the output that you think would help? |
Posted in: Starterator → Starterator Text updates
Link to this post | posted 05 Aug, 2016 01:07 | |
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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:
then enter this command:
let me know if that works of fails, that worked on my version of the SEA2016 VM |
Posted in: Starterator → Beta Version 1.1.1 released
Link to this post | posted 04 Aug, 2016 16:23 | |
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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. |
Posted in: Starterator → Beta Version 1.1.1 released
Link to this post | posted 04 Aug, 2016 03:58 | |
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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. |
Posted in: Starterator → Beta Version 1.1.1 released
Link to this post | posted 30 Jul, 2016 03:42 | |
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Ok tried jabith once and it worked all the way through so I posted the results here. That was with the original version. As with Sprinklers I will try with the beta version see if I can get it to crash there. I will let you know how those go, please if you have time try the solutions suggested above as well and let me know if those stop the crashing. |
Posted in: Starterator → phage that crash starterator
Link to this post | posted 30 Jul, 2016 03:38 | |
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OK, I tested Sprinklers on the original version of Starterator and it did not crash. You can download that report from this link. I tested it on Beta version next and it did not crash the first time but when I tried again it did crash. You can download the output from the first run of the beta version with the yellow and green starts from this link. These intermittent problems are very difficult to track down. Can you try the troublshooting solutions given in the first post of the "Read First: Common Starterator Troubleshooting" thread and report back it any of those helped. I wonder if it the problem with either the memory (which can easily change from run to run) or maybe the "Intermediate Files" issue. |
Posted in: Starterator → phage that crash starterator