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rmhubley / RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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documentation out of date? #182

Closed dgordon562 closed 1 year ago

dgordon562 commented 1 year ago

http://repeatmasker.org/RepeatMasker/ says: Install RepeatMasker Libraries RepeatMasker comes with a copy of the curated portion of Dfam ( Libraries/Dfam.h5 ) and will work out-of-the box with this library. This is a small library ( at this time ). There are two options for supplementing the main RepeatMasker library: The complete Dfam ( curated and uncurated families ) library may be downloaded from www.dfam.org in famdb HDF5 format and used to replace the distributed "Libraries/dfam.h5" file. For example: wget https://www.dfam.org/releases/Dfam_3.6/families/Dfam.h5.gz gunzip Dfam.h5.gz mv Dfam.h5 /usr/local/RepeatMasker/Libraries NOTE: This will overwrite the distributed Dfam.h5 file.

However, wget https://www.dfam.org/releases/Dfam_3.6/families/Dfam.h5.gz gives: HTTP request sent, awaiting response... 404 Not Found 2022-10-05 16:46:19 ERROR 404: Not Found.

There is a file there Dfam-p1.h5.gz but then the rest of the instructions would need to be updated: gunzip Dfam-p1.h5.gz mv Dfam-p1.h5 /usr/local/RepeatMasker/Libraries

Would that work? Would RepeatMasker look for Dfam-p1.h5 ?

rmhubley commented 1 year ago

Symlinks were missing with the standard names. This has been fixed.