Notes on setting up MAKER2
This is a quick reference for installing the parallel version of Maker2. I wrote this a while back (about 3 years) but could be useful still. Some of the tools could have undergone major updates in that timeframe.
Software
If downloading RepBase with repeatmasker, register at site first link
Will use GeneMark instead of FGENESH, and blast execs (NCBI toolkit) instead of WUBLAST
Also install GeneMark for prokaryotic (has exec gmhmmp) if annotating prokaryotic
Executables: exonerate, formatdb, and blastall must also be present, but installation not included here
Installation
mpich-3.2.tar.gz
Important to enable shared libraries, gcc is standard for Linux. Use --prefix to prevent installation in root dirs
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tar -xvf mpich-3.2.tar.gz
cd mpich-3.2/
./configure --prefix=$PWD/execs --enable-sharedlibs=gcc
Continue with installation.
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make
make install
Executables should be in bin/execs. Test using ./mpiexec -n 2 echo hello
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hello
hello
Source to bashrc so don’t have to type the path later when MAKER2 asks.
maker-2.31.8.tgz
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tar -xvf maker-2.31.8.tgz
cd maker/src
perl Build.PL
## Y to mpi install
Install PERL dependencies
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./Build installdeps
## Y to local install
Open file vi locations. Find path to Repbase for specific OS e.g. Linux , then change url to latest version, e.g.: ‘http://www.girinst.org/server/RepBase/protected/repeatmaskerlibraries/repeatmaskerlibraries-20150807.tar.gz’ because the old one won’t work with the username and password
Install SNAP and RepeatMasker, etc (alternatively just source them if they’re already installed so MAKER2 will know)
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./Build installexes
## enter username and password for RepBase
./Build status ## to see install status, should see OK, verified, enabled, etc
./Build install
Executables should be in maker/bin , NOT maker/src/bin
augustus-3.2.2.tar.g
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tar -xvf augustus-3.2.2.tar.gz
cd apps/augustus-3.2.2
make
## make install if you're an admin
Source in bashrc
gm_et_linux_64.tar.gz
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tar -xvf gm_et_linux_64.tar.gz
cd gm_et_linux_64/gmes_petap
cp gm_key ~/.gm_key ## copy license to home
Source in bashrc
tRNAscan-SE.tar.Z
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tar -xvf tRNAscan-SE.tar.Z
cd tRNAscan-SE-1.23
Edit the Makefile using vi Makefile
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BINDIR = /home/mbr/apps/tRNAscan-SE-1.23/bin
LIBDIR = /home/mbr/apps/tRNAscan-SE-1.23/lib/tRNAscan-SE
MANDIR = /home/mbr/apps/tRNAscan-SE-1.23/man
Correct the getline error during compilation in Linux
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perl -pi -e "s/getline/getline2/g" sqio.c
This changes all getline to getline2 since getline is an environmental variable in Linux
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make
make install
Source in bashrc
ncbi-blast-2.4.0+
Just unpack it, and test. Source in bashrc
snoscan.tar.gz
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tar -xvf snoscan.tar.gz
Build squid first
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cd snoscan-0.9b/squid-1.5j
Set everything to squid dir using vi Makefile
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SQUIDHOME = $(PWD)/lib/squid
BINDIR = $(PWD)/bin
SCRIPTDIR = $(PWD)/scripts
MANDIR = $(PWD)/man
Correct compile error (same as above)
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perl -pi -e "s/getline/getline2/g" sqio.c
Install
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make
make install
cd ..
make
Source in bashrc
Test MAKER2 installation
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cd ~
mkdir maker
cd maker
cp -r /path/to/maker/data/ .
maker -CTL
Edit maker_opts.ctl
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genome=data/dpp_contig.fasta
est=data/dpp_est.fasta
protein=data/dpp_protein.fasta
Check paths in maker_exe.ctl, should have the expected paths of other tools, if not, source tools, or edit this file
No mpi
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time maker
Will see this warning:
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Argument "2.53_01" isn't numeric in numeric ge (>=) at /home/mbr/apps/maker/bin/../perl/lib/forks.pm line 1570.
This does not affect maker run as far as I can see.. time. Outputs in dpp_contig.maker.output, i.e. genome+”maker.output”
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real 1m11.850s
user 1m33.228s
sys 0m5.048s
With mpi time mpiexec -n 5 maker -base=withMpi
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real 0m30.808s
user 0m52.076s
sys 0m3.592s
Output
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cd withMpi.maker.output/
Generate gff3 files
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gff3_merge -n -d withMpi_master_datastore_index.log
Generate fasta annotation files
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fasta_merge -d withMpi_master_datastore_index.log