SEA-PHAGES | Starterator completely bricked

Link to this post \| posted 17 Sep, 2016 21:18
jparker	Hi Chris, Somehow I have completely bricked Starterator. The student version gives me an error "Startstaerator has encountered an error. Please try again." Yes it says "Startstaerator". The Faculty version, where I installed the v1.1.1 now does not even have a responsive icon, just a blank white icon, and nothing happens when clicked on. I tried to start from scratch and install in the Admin version, and same as above. Help! Jordan 229Kb

Link to this post | posted 17 Sep, 2016 21:18

Hi Chris,

Somehow I have completely bricked Starterator. The student version gives me an error "Startstaerator has encountered an error. Please try again." Yes it says "Startstaerator". The Faculty version, where I installed the v1.1.1 now does not even have a responsive icon, just a blank white icon, and nothing happens when clicked on. I tried to start from scratch and install in the Admin version, and same as above.

Help!
Jordan

Link to this post \| posted 19 Sep, 2016 16:40
cdshaffer	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 Edited 19 Sep, 2016 16:46

Link to this post | posted 19 Sep, 2016 16:40

cdshaffer

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

Edited 19 Sep, 2016 16:46

Link to this post \| posted 19 Sep, 2016 20:18
jparker	Thanks Chris! It looks like I accidentally deleted something important… Unless you have a quick fix, it might be easiest for me to download and reinstall the VM, then starterator beta. Thanks for the starterator output data! seastudent@SEA2016:~$ /home/seastudent/Application/Starterator/starterator/sharterator.sh bash: /home/seastudent/Application/Starterator/starterator/sharterator.sh: No such file or directory best, jordan

Link to this post | posted 19 Sep, 2016 20:18

jparker

Thanks Chris! It looks like I accidentally deleted something important… Unless you have a quick fix, it might be easiest for me to download and reinstall the VM, then starterator beta. Thanks for the starterator output data!

seastudent@SEA2016:~$ /home/seastudent/Application/Starterator/starterator/sharterator.sh
bash: /home/seastudent/Application/Starterator/starterator/sharterator.sh: No such file or directory

best,
jordan

Link to this post \| posted 20 Sep, 2016 14:41
cdshaffer	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 `sudo apt-get upgrade` add this "–fix-missing" to the command so it looks like this: `sudo apt-get –fix-missing upgrade` 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: `bash installBetaStarterator.sh` 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.

Link to this post | posted 20 Sep, 2016 14:41

cdshaffer

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

sudo apt-get upgrade

add this "–fix-missing" to the command so it looks like this:

sudo apt-get –fix-missing upgrade

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:

bash installBetaStarterator.sh

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.

Link to this post \| posted 21 Sep, 2016 00:25
cdshaffer	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

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Starterator completely bricked