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

This page was last updated on Sunday, 22-Oct-2017 22:11:02 CDT

Installation notes for BUSCO version 3.0.2b

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Prerequisites

Installation

  1. $ cd /usr/local/bin
  2. $ git clone https://gitlab.com/ezlab/busco.git
  3. $ cd busco
  4. $ sudo python setup.py install 
    running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/busco
copying src/busco/TranscriptomeAnalysis.py -> build/lib.linux-x86_64-2.7/busco
copying src/busco/BuscoAnalysis.py -> build/lib.linux-x86_64-2.7/busco
copying src/busco/GeneSetAnalysis.py -> build/lib.linux-x86_64-2.7/busco
copying src/busco/__init__.py -> build/lib.linux-x86_64-2.7/busco
copying src/busco/GenomeAnalysis.py -> build/lib.linux-x86_64-2.7/busco
copying src/busco/BuscoConfig.py -> build/lib.linux-x86_64-2.7/busco
copying src/busco/_version.py -> build/lib.linux-x86_64-2.7/busco
creating build/lib.linux-x86_64-2.7/pipebricks
copying src/pipebricks/Toolset.py -> build/lib.linux-x86_64-2.7/pipebricks
copying src/pipebricks/__init__.py -> build/lib.linux-x86_64-2.7/pipebricks
copying src/pipebricks/PipeLogger.py -> build/lib.linux-x86_64-2.7/pipebricks
copying src/pipebricks/PipeConfig.py -> build/lib.linux-x86_64-2.7/pipebricks
copying src/pipebricks/PipeHelper.py -> build/lib.linux-x86_64-2.7/pipebricks
running install_lib
copying build/lib.linux-x86_64-2.7/pipebricks/Toolset.py -> /usr/local/lib/python2.7/dist-packages/pipebricks
copying build/lib.linux-x86_64-2.7/pipebricks/__init__.py -> /usr/local/lib/python2.7/dist-packages/pipebricks
copying build/lib.linux-x86_64-2.7/pipebricks/PipeLogger.py -> /usr/local/lib/python2.7/dist-packages/pipebricks
copying build/lib.linux-x86_64-2.7/pipebricks/PipeConfig.py -> /usr/local/lib/python2.7/dist-packages/pipebricks
copying build/lib.linux-x86_64-2.7/pipebricks/PipeHelper.py -> /usr/local/lib/python2.7/dist-packages/pipebricks
copying build/lib.linux-x86_64-2.7/busco/TranscriptomeAnalysis.py -> /usr/local/lib/python2.7/dist-packages/busco
copying build/lib.linux-x86_64-2.7/busco/BuscoAnalysis.py -> /usr/local/lib/python2.7/dist-packages/busco
copying build/lib.linux-x86_64-2.7/busco/GeneSetAnalysis.py -> /usr/local/lib/python2.7/dist-packages/busco
copying build/lib.linux-x86_64-2.7/busco/__init__.py -> /usr/local/lib/python2.7/dist-packages/busco
copying build/lib.linux-x86_64-2.7/busco/GenomeAnalysis.py -> /usr/local/lib/python2.7/dist-packages/busco
copying build/lib.linux-x86_64-2.7/busco/BuscoConfig.py -> /usr/local/lib/python2.7/dist-packages/busco
copying build/lib.linux-x86_64-2.7/busco/_version.py -> /usr/local/lib/python2.7/dist-packages/busco
byte-compiling /usr/local/lib/python2.7/dist-packages/pipebricks/Toolset.py to Toolset.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/pipebricks/__init__.py to __init__.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/pipebricks/PipeLogger.py to PipeLogger.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/pipebricks/PipeConfig.py to PipeConfig.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/pipebricks/PipeHelper.py to PipeHelper.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/busco/TranscriptomeAnalysis.py to TranscriptomeAnalysis.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/busco/BuscoAnalysis.py to BuscoAnalysis.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/busco/GeneSetAnalysis.py to GeneSetAnalysis.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/busco/__init__.py to __init__.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/busco/GenomeAnalysis.py to GenomeAnalysis.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/busco/BuscoConfig.py to BuscoConfig.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/busco/_version.py to _version.pyc
running install_egg_info
Removing /usr/local/lib/python2.7/dist-packages/BUSCO-3.0.2.egg-info
Writing /usr/local/lib/python2.7/dist-packages/BUSCO-3.0.2.egg-info
  5. Add to default PATH
    $ sudo nano /etc/profile
    …
    PATH="$PATH:/usr/local/bin/busco/scripts"
    …
  6. Update default configuration file
    $ nano config/config.ini.default 
    …
[augustus]
# path to augustus
path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/bin//usr/local/bin/augustus/bin/

[etraining]
# path to augustus etraining
path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/bin//usr/local/bin/augustus/bin/

# path to augustus perl scripts, redeclare it for each new script
[gff2gbSmallDNA.pl]
path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/scripts//usr/local/bin/augustus/scripts/
[new_species.pl]
path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/scripts//usr/local/bin/augustus/scripts/
[optimize_augustus.pl]
path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/scripts//usr/local/bin/augustus/scripts/

[hmmsearch]
# path to HMMsearch executable
path = /home/osboxes/BUSCOVM/hmmer/hmmer-3.1b2-linux-intel-ia32/binaries//usr/local/bin/
…
  7. Make a local copy of documentation
    $ wget http://gitlab.com/ezlab/busco/raw/master/BUSCO_v3_userguide.pdf
  8. $ mv BUSCO_v3_userguide.pdf /programinstallers/web/programs/busco/