there are few pre-requisite things to install repeatmasker..
repeatmasker is the first step involved in the est assembly pipeline
the prerequisites are
----perl
----sequence search engine
you can install one of the three search engines present
-cross-match
-rm blast ( i am using this one) http://www.repeatmasker.org/RMBlast.html
-abblast/wublast (these requires licensing )
Try 1. Download pre-compiled versions
$ wget http://www.repeatmasker.org/rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz
$ tar zxvf rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz
$ cd rmblast-1.2-ncbi-blast-2.2.23+
$ cd bin
$ ./rmblastn
./rmblastn: error while loading shared libraries: libpcre.so.0: cannot open shared object file:
No such file or directory
I am unable to install this library. Things i found out, i may be wrong
* libpcre is part of the 32-bit libraries
* on ubuntu i was unable to find the library, maybe because of the repository.
Try 2. Download RMBlast source
$ wget http://www.repeatmasker.org/rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz
$ tar zxvf rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz
$ cd rmblast-1.2-ncbi-blast-2.2.23+-src/c++
$ ./configure --with-mt --prefix=/usr/local/rmblast --without-debug
$ make
$ sudo make install
This installed good without any problem Modify ~/.bashrc to include the line below
export PATH=$PATH:/usr/local/rmblast/bin
To check installation
$ source ~/.bashrc
$ rmblastn
BLAST query/options error: Either a BLAST database or subject sequence(s) must be specified
If you get the above message then RMBlast is installed
---- tanden repeat finder (trf) is needed
The TRF download will contain a single executable file. You will need to rename the file from whatever it is to just 'trf' (all lower case). Make TRF executable by typing chmod +x+u trf. You can then move this file wherever you want. I just put it in the /RepeatMasker directory.
the next step is installing repeat database...... it takes 2 days to get registered soo temporarily this process would be out of service.................
after 1 day..........
----Repeatmasker database
* url: http://www.repeatmasker.org/RMDownload.html
* download latest release version
$ cd /usr/local
$ wget http://www.repeatmasker.org/RepeatMasker-open-3-2-9.tar.gz
$ tar zxvf RepeatMasker-open-3-2-9.tar.gz
* It requires RepeatMasker Libraries
o url: http://www.girinst.org/
o Go to Downloads > RepeatMasker libraries > RepeatMasker edition: local:
$ tar zxvf repeatmaskerlibraries-20090604.tar.gz
$ rm -rf repeatmaskerlibraries-20090604.tar.gz
$ mv Libraries/RepeatMaskerLib.embl /usr/local/RepeatMasker/Libraries/.
download RepeatMasker
unpack it
install RepeatMasker libraries..copy them into RepeatMasker main folder
now configure the RepeatMasker script by using
perl ./configure
while configuring it would ask for so many where abouts ??
perl path
trf path
after finishing installation
check whether its working or not by typing the command
RepeatMasker in terminal..
repeatmasker is the first step involved in the est assembly pipeline
the prerequisites are
----perl
----sequence search engine
you can install one of the three search engines present
-cross-match
-rm blast ( i am using this one) http://www.repeatmasker.org/RMBlast.html
-abblast/wublast (these requires licensing )
Try 1. Download pre-compiled versions
$ wget http://www.repeatmasker.org/rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz
$ tar zxvf rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz
$ cd rmblast-1.2-ncbi-blast-2.2.23+
$ cd bin
$ ./rmblastn
./rmblastn: error while loading shared libraries: libpcre.so.0: cannot open shared object file:
No such file or directory
I am unable to install this library. Things i found out, i may be wrong
* libpcre is part of the 32-bit libraries
* on ubuntu i was unable to find the library, maybe because of the repository.
Try 2. Download RMBlast source
$ wget http://www.repeatmasker.org/rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz
$ tar zxvf rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz
$ cd rmblast-1.2-ncbi-blast-2.2.23+-src/c++
$ ./configure --with-mt --prefix=/usr/local/rmblast --without-debug
$ make
$ sudo make install
This installed good without any problem Modify ~/.bashrc to include the line below
export PATH=$PATH:/usr/local/rmblast/bin
To check installation
$ source ~/.bashrc
$ rmblastn
BLAST query/options error: Either a BLAST database or subject sequence(s) must be specified
If you get the above message then RMBlast is installed
---- tanden repeat finder (trf) is needed
The TRF download will contain a single executable file. You will need to rename the file from whatever it is to just 'trf' (all lower case). Make TRF executable by typing chmod +x+u trf. You can then move this file wherever you want. I just put it in the /RepeatMasker directory.
the next step is installing repeat database...... it takes 2 days to get registered soo temporarily this process would be out of service.................
after 1 day..........
----Repeatmasker database
* url: http://www.repeatmasker.org/RMDownload.html
* download latest release version
$ cd /usr/local
$ wget http://www.repeatmasker.org/RepeatMasker-open-3-2-9.tar.gz
$ tar zxvf RepeatMasker-open-3-2-9.tar.gz
* It requires RepeatMasker Libraries
o url: http://www.girinst.org/
o Go to Downloads > RepeatMasker libraries > RepeatMasker edition: local:
$ tar zxvf repeatmaskerlibraries-20090604.tar.gz
$ rm -rf repeatmaskerlibraries-20090604.tar.gz
$ mv Libraries/RepeatMaskerLib.embl /usr/local/RepeatMasker/Libraries/.
download RepeatMasker
unpack it
install RepeatMasker libraries..copy them into RepeatMasker main folder
now configure the RepeatMasker script by using
perl ./configure
while configuring it would ask for so many where abouts ??
perl path
trf path
after finishing installation
check whether its working or not by typing the command
RepeatMasker in terminal..
-bash: RepeatMasker: command not found
ReplyDeleteAny suggestions?
duh. forgot to add ./
ReplyDeleteI installed and configured automatically successfuly RepeatMasker in my computer (platform linux-ubuntu). My search machine is cross_macth (default).
ReplyDeleteBut, I can not run the program, because when I type any command line in the Terminal, always get the following message: "RepeatMasker: command not Found".
For example:
root@ricardom: “RepeatMasker -div 10 -alu 1_sapiens.fasta”
root@ricardom: “RepeatMasker: command not found”
I' ve tried different combinations of command lines, with uppercase and lowercase letters, and have reconfigured several times RepeatMasker, but can not run the program. Curiously, some command lines work well, for example "../RepeatMasker" or "../RepeatMasker -help".
I think that the program is correctly installed.
I read the RepeatMasker's help (and other texts that i found on the internet), but I have not found a solution for this case.
Please, help me to resolve this case.
Best Regards,
R.M.
I am not able to find crossmatch code. Please send me download link for cross-match
ReplyDeleteI think you have to follow the instruction here to get a copy of cross_match, it will be distributed with phrep, phrap.
Deletehttp://www.phrap.org/consed/consed.html#howToGet
good luck with that. :)
This comment has been removed by the author.
ReplyDeleteHi, I got this when I run RepeatMasker. This is where trf runs and the file trfResults-1402725429-7976.err shows:
ReplyDeleteError: /repeatmasker/RM_8444.SatJun141557072014/su.fasta_batch-1.masked not found.
I checked in the RM_8444.SatJun141557072014 folder, it does have su.fasta_batch-1.masked file there.
Do you know why this happened? Why trf can't find the file even it is there? Thanks.