To use this feature, you must have MPICH2 installed with the the
--enable-sharedlibs flag set during installation (See MPICH2
Installer’s Guide). I have installed this for you. So lets set up
MPI_MAKER and run the example file that comes with MAKER.
cd ~/Documents/Software/maker/MPI
perl Install.PL
You should now see the executable mpi_maker listed among the all the
MAKER scripts (/maker/bin). Let’s run some example data to see if
MPI_MAKER is working properly.
cd ~
mkdir ~/maker_run2
cd maker_run2
cp ~Documents/Software/maker/data/dpp_* ~/maker_run2
maker -CTL
gedit maker_opts.ctl
Set values in maker configuration files.
genome:dpp_contig.fasta
est:dpp_transcripts.fasta
protein:dpp_proteins.fasta
predictor:snap
snaphmm:fly
We need to set up a few more things for MPI to work. Type mpd to see a
list of instructions.
mpd
You should see the following.
configuration file /home/gmod/mpd.conf not found
A file named .mpd.conf file must be present in the user's home
directory (/etc/mpd.conf if root) with read and write access
only for the user, and must contain at least a line with:
MPD_SECRETWORD=<secretword>
One way to safely create this file is to do the following:
cd $HOME
touch .mpd.conf
chmod 600 .mpd.conf
and then use an editor to insert a line like
MPD_SECRETWORD=mr45-j9z
into the file. (Of course use some other secret word than mr45-j9z.)
Follow the instructions to set this file up, and start the mpi
environment with mpdboot. Then run mpi_maker through the MPI manager
mpiexec.
mpdboot
mpiexec -n 2 mpi_maker
mpiexec is a wrapper that handles the MPI environment. The -n 2 flag
tells mpiexec to use 2 cpus/nodes when running mpi_maker. For a
large cluster, this could be set to something like 100. You should now
know how to start a MAKER job via MPI.
The MWAS interface provides a very convenient method for running MAKER and viewing results; however, because compute resources are limited users are only allowed to submit a maximum of 2 megabases of sequence per job. So while MWAS might be suitable for some analyses (i.e. annotating BACs and short preliminary assemblies), if you plan on annotating an entire genome you will need to install MAKER locally. But if you like the convenience of the MWAS user interface, you can optionally install the interface on top of a locally installed version of MAKER for use in your own lab.
First under the maker directory there is a subdirectory called MWAS.
MWAS contains all the needed files to build the MAKER web interface.
The maker/MWAS/bin/mwas_server file is used to setup and run this web
interface. Lets configure that now. There are three steps to setting up
the server. First you must create and edit a server configuration file,
then load all other configuration files, and then install all files to
the appropriate web accessible directory.
cd /home/gmod/Documents/Software/maker/MWAS/
bin/mwas_server PREP
This will create a file in /maker/MWAS/config/ called server.ctl. We
will need to edit this file before continuing.
gedit config/server.ctl
Set:
apache_user:www-data
web_address:http://localhost
cgi_dir:/usr/lib/cgi-bin/maker
cgi_web:/cgi-bin/maker
html_dir:/var/www/maker
html_web:/maker
data_dir:/var/www/maker/data
use_login:0
JBROWSE_ROOT:/var/www/jbrowse/
GBROWSE_MASTER:/etc/gbrowse2/GBrowse.conf
Now we need to generate other settings that are dependent on the values
in server_opts.ctl.
bin/mwas_server CONFIG
Several new configuration files should now be loaded in the config/
directory. These new files define default MAKER options for the server
and the location of files for the server dropdown menus.
maker_bopts.ctl
maker_exe.ctl
maker_opts.ctl
menus.ctl
We only need to edit one of these files to let MAKER know to use NCBI BLAST instead of WUBLAST.
emacs maker_bopts.ctl
blast_type:ncbi
Now finally lets copy all web related files to the appropriate web
accessible directories. This must be done as root or using sudo.
sudo bin/mwas_server SETUP
If you set APOLLO_ROOT in the server.ctl file, then you can now
setup a special Java Web Start version of Apollo to
view results directly from the web interface. Web Start will be
described in more detail in the Apollo session. This must be done as
root or using sudo.
sudo bin/mwas_server APOLLO
In addition, if you have JBrowse and GBrowse 2 installed you can also
use these to view results. To use these you must have JBROWSE_ROOT and
GBROWSE_MASTER set in the server.ctl file (already set). Then we
tell mwas_server to configure the programs.
sudo bin/mwas_server GBROWSE
sudo bin/mwas_server JBROWSE
We can now run MAKER examples using this web interface, but first we need to launch a server daemon to monitor for new job submissions.
sudo bin/mwas_server START
And then go to
MAKER comes with a number of accessory scripts that are meant to assist in manipulations of the MAKER input and output files.
Scripts:
add_utr_gff.pl <gff3_directory>
add_utr_start_stop_gff <gff3_file>
fasta_merge -d <datastore_index> -o <outfile>
gff3_merge -d <datastore_index> -o <outfile>
gff3_2_gtf <gff3_file>
gff3_preds2models <gff3 file> <pred list>
iprscan2gff3 <iprscan_file> <gff3_fasta>
iprscan_batch <file_name> <cpus> <log_file>
ipr_update_gff <gff3_file> <iprscan_file>
maker2zff.pl <gff3_file>
maker_functional_fasta <uniprot_fasta> <blast_output> <fasta1> <fasta2> <fasta3> ...
maker_functional_gff <uniprot_fasta> <blast_output> <gff3_1>
maker_map_ids --prefix PYU1_ --justify 6 genome.all.gff > genome.all.id.map
map_fasta_ids <map_file> <fasta_file>
map_gff_ids <map_file> <gff3_file>
split_fasta [count] <input_fasta>
Facts about “MAKER Tutorial 2010”
| Has topic | MAKER + |