After yesterday’s difficulties getting RMblast to compile, I deleted the folder and went through the build process again.

This time it worked, but it did not put rmblastn in the specified location (/home/shared/rmblast).

This fact took me a fair amount of time to figure out. Finally, after a couple of different re-builds, I ran find to see if rmblastn existed somewhere I wasn’t looking:

Additionally, I couldn’t find the location of the various BLAST executables. Some internet sleuthing led me to the NCBI page on installing BLAST+ from source, which indicates that the executables are stored in:

ncbi-blast-VERSION+-src/c++/ReleaseMT/bin/

How intuitive! /s

In order to improve readability and usability of the /home/shared/ directory, I renamed the /home/shared/rmblast directory to reflect the BLAST version and created a symbolic link in that directory to the rmlbastn executable:

Symbolic link to RMBLAST

Initiate RepeatMasker configuration


Confirm perl install location:


Confirm RepeatMasker install location:


Specify TRF install location:


Hmmm, TRF error. Looking for file called trf:


Renamed TRF file to trf and now it’s automatically found:


Set RMBlast as search engine:


Set RMBlast install location:


Set RMBlast as default search engine:


Confirmation of RMBlast as default search engine and successful installation of RepeatMasker:


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

Software Installation – RepeatMasker v4.0.7 on Emu/Roadrunner Continued
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