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

Unfortunately, the 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).

Installed RepeatMasker:

4. Downloaded RepeatMasker 4.0.7

- Saved to ```/home/shared/RepeatMasker-4.0.7```

5. Installed RepBase RepeatMasker Edition 20170127 in /home/shared//home/shared/RepeatMasker-4.0.7/Libraries

Currently re-building RMBlast and it takes forever… Will report back when I have it running.

from Sam’s Notebook https://ift.tt/2IFRP79

Software Installation – RepeatMasker v4.0.7 on Emu/Roadrunner
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