Link to this post | posted 10 Jan, 2017 02:34

cdshaffer

Curious, It is entirely possible there is a bug in the code that I added when going to v1.1 from the that beta version. I tested my most recent version and it did not crash on beardedlady. Unfortunately I am in the middle of updating the part of starterator that generates the pdf report. I got most of the issues with the single pham reports the way I want them but I have not updated the code to handle the "all phage" reports. I have posted the most recent version of a whole phage report here: phages.wustl.edu/BeardedLady_DraftReport.pdf but you can see there is still a lot I need to add back into the reports before they are useful again. It does have all the graphics tracks its just missing all the summary reports on annotated starts and all that. If you just use the graphical tracks the whole report should work, if you want all the text summary you will just have to stick with the beta version or go to phages.wustl.edu/starterator and get the pham report for each pham in the phage one by one.

Link to this post | posted 10 Jan, 2017 01:15

cdshaffer

Sorry I did get a chance to write some new code for starterator over thanksgiving in hopes of getting things into the VM but it was just not soon enough given the timing of the in silico workshop and the need to get the VM out to everyone attending. So if you are using the SEA 2017 and have not updated manually (using git command line), you still have the original version. You can still use the SEA 2017 VM but you will not get any of my updates. The current best way to get those reports is to use the pham reports I have been posting on the web. I post new reports every time there is a new phamerator database and I use my most recent code (for good or bad). To get those you can go here http://phages.wustl.edu/starterator to see a list of all the pham reports (for all phams with two or more members). Just scroll down till you find the link for the pham you are interested in and click the link. However given the length of the list, an easier technique is to just type in the address using the pham number since everything else in the address is identical. For example to get to the report for pham 21476 just type in this address http://phages.wustl.edu/starterator/Pham21476Report.pdf And if you want pham 66 just replace the 21476 in the above address with 66: http://phages.wustl.edu/starterator/Pham66Report.pdf

Link to this post | posted 10 Jan, 2017 01:07

cdshaffer

Sorry everyone but I had some free time to write code over thanksgiving in hopes of getting things into the VM but it was just not soon enough given the timing of the in silico workshop and the need to get the VM out to everyone attending. So if you are using the SEA 2017 and have not updated manually (using git command line), you still have the original version which does crash on quite a few phams. The current best way to get reports if the SEA 2017 VM crashes on your phage is to use the pham reports I have been posting on the web. I post new reports every time there is a new phamerator database and I use my most recent code so you might find them better than what you are getting from the VM. You can go here http://phages.wustl.edu/starterator to see a list of all the pham reports for all phams with two or more members, simply scroll down till you find the link for the pham you are interested in and click the link. However given the length of the list, an easier technique is to just type in the address using the pham number since everything else in the address is identical. For example to get to the report for pham 21476 just type in this address http://phages.wustl.edu/starterator/Pham21476Report.pdf

Link to this post | posted 02 Dec, 2016 23:08

cdshaffer

Everyone, I am happy to announce the release of version 1.1 of Starterator. This has several minor updates and bug fixes. It is available now from github.com/SEA-PHAGES/starterator. I have let Dan know and I expect he aleady has or will very soon the new SEA 2017 VM to this new version. I will be collaborating with Dan to create an update script which can be run to update the Starterator currently installed on a working VM. New features: 1. Better recognition of identical tracks which are then collapsed into a single track. Many phams now have significantly fewer tracks. 2. Tracks are now labeled with the name of the first phage on the list and indicate how many other phage are also represented in the track 3. Tracks now indicate the called start with a yellow bar if the start is Draft quality and a green bar if the start is based on published annotations 4. The report has been updated in several ways: A. The report now indicates the start which has been most often called in the published annotations and does not consider draft quality annotations when looking for the "most annotated" start. B. The "suggested starts" section has been depreciated as it was too often based on draft annotations which simply perpetuated the original Glimmer/Genemark calls. C. The run date has been added to the output so that changes in the phamerator database can be easily recognized and the most recent report used for analysis. 5. Many minor bugfixes We will post update info for those that wish to continue to use older VM's soon.

Link to this post | posted 02 Dec, 2016 22:33

cdshaffer

I would recommend that you update the VM this year as security updates for the old VM will be stopping sometime in 2017. This is why there is a new SEA VM. The new version uses Ubuntu 14.04 has updates through at least 2019. Web Phamerator will be available this spring but it is unknown how many features will make it into the final version. It can already make comparison maps and it is quite a bit faster so I will be using it in class ad the default. However, it is unclear how many of the advanced features will make it into the web version this year. For my class I have requested that VM be installed but I did that mostly for back-up (in case the network goes down) and access to advanced features (like access to the complete pham table).

Link to this post | posted 15 Nov, 2016 21:11
cdshaffer	NCBI has changed their website so that DNA Master cannot connect. You need to run the update DNA Master under the help menu and restart DNA Master to get to the newest version. Be sure to post if you have problems.

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

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 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 01 Sep, 2016 17:36
cdshaffer	OK I will look into this, see if I can replicate the issue.