ILRI Research Computing

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====== BUSCO ======
BUSCO (Benchmarking Universal Single-Copy Orthologs) assesses genome assembly and annotation completeness with single-copy ortholog.

===== Information =====

  * Latest Version: 5.2.2
  * Added: August, 2015
  * Updated: December, 2021
  * Link: https://busco.ezlab.org

===== Usage =====

See versions of BUSCO which are available:
<code>$ module avail BUSCO</code>

Load one version into your environment and run it:
<code>$ module load BUSCO/5.2.2</code>

After loading the module, consult the built-in help:

<code>$ busco -h</code>

See the BUSCO documentation for more information about how to use it: https://busco.ezlab.org/busco_userguide.html#running-busco

Note: BUSCO utilizes Augustus and requires you to make a copy of the Augustus configuration for each of your runs as well as set up an environment variable pointing to it, ie:

<code>$ cp -r /export/apps/augustus/3.2.3/config /var/scratch/aorth-augustus-config
$ export AUGUSTUS_CONFIG_PATH=/var/scratch/aorth-augustus-config</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ cd /tmp
$ wget https://gitlab.com/ezlab/busco/-/archive/5.2.2/busco-5.2.2.tar.gz
$ tar xf busco-5.2.2.tar.gz 
$ cd busco-5.2.2
$ sudo mkdir /export/apps/BUSCO/5.2.2
$ sudo chown aorth /export/apps/BUSCO/5.2.2
$ python3 -m venv /export/apps/BUSCO/5.2.2
$ source /export/apps/BUSCO/5.2.2/bin/activate
$ pip install --upgrade setuptools pip
$ pip install pandas biopython
$ python setup.py install
$ sudo cp scripts/generate_plot.py /export/apps/BUSCO/5.2.2/bin
$ module load R/4.0
$ mkdir /export/apps/BUSCO/5.2.2/r-libs
$ R_LIBS=/export/apps/BUSCO/5.2.2/r-libs Rscript -e 'install.packages("ggplot2", repos="https://cran.rstudio.com")'
$ sudo chown -R root:root /export/apps/BUSCO/5.2.2</code>