Steven asked that I re-run some Olympia oyster transposable elements analysis using RepeatMasker and a newer version of our Olympia oyster genome assembly.
Installed the software on both of the Apple Xserves (Emu and Roadrunner) running Ubuntu 16.04.
Followed the instructions outlined here:
Starting with the prerequisites:
1. Download and install RMBlast
- NCBI Blast 2.6.0 source - isb 2.6.0 patch
make command continually failed:
cd /home/shared/ncbi-blast-2.6.0+-src/c++ make
While trying to troubleshoot this issue, continued with the other prerequisites:
2. Downloaded Tandem Repeat Finder v.4.09
- Saved file (```trf409.linux64```) to ```/home/shared/bin```. NOTE: ```/home/shared/bin``` is part of the system PATH. See the ```/etc/environment``` file. - Changed permissions to be executable: <pre><code>sudo chmod 775 trf409.linux64</code></pre>
3. Downloaded RepBase RepeatMasker Edition 20170127 (NOTE: This requires registration in order to obtain a username/password to download the file).
4. Downloaded RepeatMasker 4.0.7
- Saved to ```/home/shared/RepeatMasker-4.0.7```
5. Installed RepBase RepeatMasker Edition 20170127 in
Currently re-building RMBlast and it takes forever… Will report back when I have it running.