The Test Case - EvidentialGene Part 2

    To ensure you can run tr2aacds, the EvidentialGene website provides you with a test case before you run the pipeline on your own data. This allows you to troubleshoot any problems you may encounter. Here is a link to the test case files:

• http://arthropods.eugenes.org/EvidentialGene/plants/arabidopsis/evigene_tr2aacds_test/

    I wouldn't recommend using the run file it gives you in there, as it gave me quite a bit of trouble. The only file I downloaded was the evigene_tr2aacds_test2021.tar.gz file to compare outputs. I ran into a problem because the download wasn't working with the arath_TAIR10_20101214up.cdna.gz file that I needed to run tr2aacds on for the test.

(from the evigene_tr2aacds_test directory)

The link that I'm hovering over didn't download anything, but instead brought me to a page with what looked like the contents of the file:

(from the arath_TAIR10_20101214up.cdna.gz link)

    Whether or not that was intended, I needed the file so that I could run the test case. This is where the SourceForge downloads page comes in. This site is linked on the EvidentialGene page as well. I clicked the "Files" tab and then chose the evigene_tr2aacds_test directory; here, I found the arath_TAIR10_20101214up.cdna.gz I needed, and the run file or tr2aacds_test.sh as well. run_tr2aacds.sh, shown in the first image, is the run file I originally tried using, but the one on SourceForge is what I eventually had to use. Here is where I downloaded the main evigene software required for tr2aacds by clicking the main download button (big and green).

(from the SourceForge page)

    Now that I had the genome data, evigene, and run files for the test case, I needed to get the proprietary software mentioned in the first post. This process will be detailed in the next post.

Navigating The Website - EvidentialGene Part 1

    Note: The following few posts on this project are not in real-time, but are separated into parts so that I can show how I progressed chronologically; i.e., I didn't blog this project while I was doing it.

    Disclaimer: Please do not take anything I say in these posts as professional advice and/or criticism. I do not have a higher education degree in the topics I'll be indulging in the next few posts.

    My plan going into this was to simply use EvidentialGene to magically join together two genome assemblies. This was not the case. At least, not the simple and magical part.

    The system I've done all this on is running Ubuntu 22.04 LTS. I think it's a reasonable choice since there isn't much bloatware, and I can easily run things from the terminal. Getting to the website with my goal in mind, I came upon a confusing sight. It's not very user-friendly in my opinion, but then again this was my first time using something akin to it. After some digging, I figured out that I'd need to use the tr2aacds pipeline to combine my assemblies together. I gleaned quite a bit of the info to come to this conclusion from these links: 

• the About page for Evigene, http://arthropods.eugenes.org/EvidentialGene/evigene/
• the blog/discussion page for Evigene on SourceForge, https://sourceforge.net/p/evidentialgene/blog/
• this video where Don Gilbert (developer of EvidentialGene) speaks on the program, https://www.youtube.com/watch?v=Lu4JqZPGKW0&ab_channel=IUPTI

    These links helped me out a lot, especially the SourceForge blog one. The About page is a little hard to learn from since the formatting and organization of topics are hard to follow in my opinion, but regardless, it is a valuable source of information. 

    Next, I needed to get the proprietary software for tr2aacds to work. These are:

(from the About page)

This part of getting all the proprietary software proved to be a bit of a hassle, as will be evident in the later posts. Thankfully a test case is provided that helps in the troubleshooting phase.