Carrot root and DNA VCRU Bioinformatics USDA ARS Vegetable Crops Research Unit

This page was last updated on Friday, 28-Dec-2018 12:35:52 CST

Installation notes for MAKER version 2.31 - Feb 11, 2014

Home Page

Prerequisites

Installation

  1. $ ver="2.31"
  2. $ cd /programinstallers/
  3. Download requires registration at home page.
    File downloaded with web browser was maker-$ver.tgz
  4. $ cd /usr/local/bin
  5. If upgrading, remove old version
    $ rm maker -rf
  6. $ tar -zxvf /programinstallers/maker-$ver.tgz
  7. $ cd maker/src
  8. $ perl Build.PL 
    Checking prerequisites...
  recommends:
    *  DBD::Pg is not installed

ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the versions
of the modules indicated above before proceeding with this installation

Run 'Build installdeps' to install missing prerequisites.


MAKER supports distributed parallelization via MPI.
Would you like to configure MAKER for MPI (This
requires that you have an MPI client installed)? [N ]y

Please specify the path to 'mpicc' on your system: [/usr/lib64/mpich2/bin/mpicc ]
/usr/lib64/mpich2/bin/mpicc 

Please specify the path to the directory containing 'mpi.h': [/usr/include/mpich2-x86_64 ]
/usr/include/mpich2-x86_64 
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'MAKER' version '2.31'


The file 'Build' has been created for you to finish installing MAKER.


==============================================================================
STATUS MAKER 2.31
==============================================================================
PERL Dependencies:	VERIFIED
External Programs:	VERIFIED
External C Libraries:	VERIFIED
MPI SUPPORT:		ENABLED
MWAS Web Interface:	DISABLED
MAKER PACKAGE:		CONFIGURATION OK


Important Commands:
	./Build installdeps	#installs missing PERL dependencies
	./Build installexes	#installs all missing external programs
	./Build install		#installs MAKER
	./Build status		#Shows this status menu

Other Commands:
	./Build repeatmasker	#installs RepeatMasker (asks for RepBase)
	./Build blast		#installs BLAST (NCBI BLAST+)
	./Build exonerate	#installs Exonerate (v2 on UNIX / v1 on Mac OSX)
	./Build snap		#installs SNAP
	./Build augustus	#installs Augustus
	./Build apollo		#installs Apollo
	./Build gbrowse		#installs GBrowse (must be root)
	./Build jbrowse		#installs JBrowse (MAKER copy, not web accecible)
	./Build webapollo	#installs WebApollo (use maker2wap to create DBs)
	./Build mpich2		#installs MPICH2 (but manual install recommended)
  9. $ ./Build install 
    Configuring MAKER with MPI support
Installing MAKER...
Configuring MAKER with MPI support
Subroutine dl_load_flags redefined at (eval 125) line 8.
Installing /dcdata1/programinstallers/maker/src/../perl/lib/MAKER/ConfigData.pm
Installing /dcdata1/programinstallers/maker/src/../perl/lib/auto/Parallel/Application/MPI/MPI.bs
Installing /dcdata1/programinstallers/maker/src/../perl/lib/auto/Parallel/Application/MPI/MPI.so
Installing /dcdata1/programinstallers/maker/src/../perl/lib/auto/Parallel/Application/MPI/MPI.inl
Installing /dcdata1/programinstallers/maker/src/../perl/lib/Parallel/Application/MPI.pm
Installing /dcdata1/programinstallers/maker/src/../perl/man/MAKER::ConfigData.3pm
Installing /dcdata1/programinstallers/maker/src/../bin/maker
Installing /dcdata1/programinstallers/maker/src/../bin/cufflinks2gff3
Installing /dcdata1/programinstallers/maker/src/../bin/map2assembly
Installing /dcdata1/programinstallers/maker/src/../bin/fasta_tool
Installing /dcdata1/programinstallers/maker/src/../bin/tophat2gff3
Installing /dcdata1/programinstallers/maker/src/../bin/maker2eval_gtf
Installing /dcdata1/programinstallers/maker/src/../bin/map_data_ids
Installing /dcdata1/programinstallers/maker/src/../bin/maker2jbrowse
Installing /dcdata1/programinstallers/maker/src/../bin/maker2chado
Installing /dcdata1/programinstallers/maker/src/../bin/mpi_iprscan
Installing /dcdata1/programinstallers/maker/src/../bin/maker_functional_fasta
Installing /dcdata1/programinstallers/maker/src/../bin/genemark_gtf2gff3
Installing /dcdata1/programinstallers/maker/src/../bin/maker_map_ids
Installing /dcdata1/programinstallers/maker/src/../bin/compare
Installing /dcdata1/programinstallers/maker/src/../bin/iprscan2gff3
Installing /dcdata1/programinstallers/maker/src/../bin/map_gff_ids
Installing /dcdata1/programinstallers/maker/src/../bin/gff3_merge
Installing /dcdata1/programinstallers/maker/src/../bin/maker2zff
Installing /dcdata1/programinstallers/maker/src/../bin/cegma2zff
Installing /dcdata1/programinstallers/maker/src/../bin/maker2wap
Installing /dcdata1/programinstallers/maker/src/../bin/ipr_update_gff
Installing /dcdata1/programinstallers/maker/src/../bin/maker_functional
Installing /dcdata1/programinstallers/maker/src/../bin/map_fasta_ids
Installing /dcdata1/programinstallers/maker/src/../bin/iprscan_wrap
Installing /dcdata1/programinstallers/maker/src/../bin/fasta_merge
Installing /dcdata1/programinstallers/maker/src/../bin/chado2gff3
Installing /dcdata1/programinstallers/maker/src/../bin/maker_functional_gff
Installing /dcdata1/programinstallers/maker/src/../bin/mpi_evaluator
Installing /dcdata1/programinstallers/maker/src/../bin/evaluator
cp blib/config-x86_64-linux-thread-multi-5.012004 /dcdata1/programinstallers/maker/src/../perl/config-x86_64-linux-thread-multi-5.012004
  10. Add to default PATH for all users
    $ sudo nano /etc/profile
    ...
    PATH="$PATH:/usr/local/bin/maker/bin"
    ...

Installation notes for MAKER container version 2.31.10--pl526_11

Home Page

  1. $ sudo apt-get install docker.io
  2. $ sudo docker pull quay.io/biocontainers/maker
    Using default tag: latest
    Error response from daemon: manifest for quay.io/biocontainers/maker:latest not found
  3. Get version from https://quay.io/repository/biocontainers/maker?tab=tags
    $ sudo docker pull quay.io/biocontainers/maker:2.31.10--pl526_11
  4. Any user wanting to run the container needs to be in the docker group
    $ sudo usermod -aG docker username
  5. log out and back in for permission change to take effect
  6. List docker images with
    $ docker images 
    docker images
REPOSITORY                    TAG                 IMAGE ID            CREATED             SIZE
quay.io/biocontainers/maker   2.31.10--pl526_11   cdc68137b16b        2 months ago        4.26GB
  7. $ docker run quay.io/biocontainers/maker:2.31.10--pl526_11 maker -h
  8. Put a batch test.sh in current directory and run it
    #!/bin/bash
cd /host
echo "Maker starting"
#maker -CTL
maker -debug &> maker.debug.log
echo "Maker done"
    $ docker run --user $(id -u):$(id -g) --volume ~/maker_tutorial/example_01_basic:/host --volume /usr/local/bin/RepeatMasker/Libraries:/Libraries quay.io/biocontainers/maker:2.31.10--pl526_11 /host/test.sh