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: 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.
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