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INSTALL
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INSTALL
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RepeatMasker Installation Notes
===============================
Pre-requisites
--------------
- A UNIX based operating system.
- Perl 5.8.0 or higher installed.
- Python 3.0 installed.
- h5py HDF5 library for Python
See https://docs.h5py.org/en/latest/build.html for installation
instructions.
- TRF 4.09 or higher ( http://tandem.bu.edu/trf/trf.html )
- A search engine. We currently support:
crossmatch : http://www.phrap.org
rmblast : http://www.repeatmasker.org/RMBlast.html
nhmmer : Pre release version -
ftp://selab.janelia.org/pub/pickup/hmmer3.1-snap20121016.1.tgz
( Dfam required )
abblast/wublast : http://blast.advbiocomp.com/licensing/
- Dfam and/or RepeatMasker libraries. The curated families from
Dfam 3.1 are included in this release. Updates and the complete
(curated & uncrated) Dfam libraries can be found at: www.dfam.org.
The RepBase RepeatMasker Library can be obtained at:
http://www.girinst.org
Installation
------------
1. Unpack the distribution in your home directory or in a location where it
may be shared with other users of your system ( ie. /usr/local/ ). Make
sure you do not extract in a directory already containing a pre-existing
directory called "RepeatMasker" as it will attempt to overwrite files
contained within. For example:
% cp RepeatMasker-open-4-#-#.tar.gz /usr/local
% cd /usr/local
% gunzip RepeatMasker-open-4-#-#.tar.gz
% tar xvf RepeatMasker-open-4-#-#.tar
2. RepeatMasker comes with a copy of the curated portion of
Dfam ( Libraries/Dfam.h5 ). 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_3.2/families/Dfam.h5.gz
% gunzip Dfam.h5.gz
## NOTE: This will overwrite the distributed Dfam.h5 file.
% mv Dfam.h5 /usr/local/RepeatMasker/Libraries
and/or
- The RepBase RepeatMasker Edition ( final version 10/26/2018 )
may be downloaded from www.girinst.org and unpaked in the
RepeatMasker directory. For example:
% cp RepBaseRepeatMaskerEdition-20181026.tar.gz /usr/local/RepeatMasker/
% cd /usr/local/RepeatMasker
% gunzip RepBaseRepeatMaskerEdition-20181026.tar.gz
% tar xvf RepBaseRepeatMaskerEdition-20181026.tar
% rm RepBaseRepeatMaskerEdition-20181026.tar
3. Configure the distribution by invoking Perl on the
the "configure" script, i.e.:
perl ./configure
The configure script will prompt you for all the
information needed to setup the RepeatMasker suite of
programs.
Library Cache Directories
-------------------------
Since version 3.0 RepeatMasker creates species-specific libraries
on the fly. These libraries are cached in the first writable
directory in the programs library path. The default path is:
1. The RepeatMasker installation "Library" directory.
2. The ".RepeatMaskerCache" subdirectory of the users home
directory.
3. The temporary processing directory "RM_#" created
in the same directory as the sequence file and
removed at the end of the run.
NOTE: If the program cannot save libraries in either path 1 or 2, the
libraries will need to be created each time the program runs. This
will slow down runs on shorter sequences.