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busco-software [2020/05/12 15:45] aorthbusco-software [2023/03/21 12:37] (current) aorth
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 ===== Information ===== ===== Information =====
  
-  * Latest Version: 4.0.6+  * Latest Version: 5.2.2
   * Added: August, 2015   * Added: August, 2015
-  * Updated: May2020+  * Updated: December2021
   * Link: https://busco.ezlab.org   * Link: https://busco.ezlab.org
  
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 Load one version into your environment and run it: Load one version into your environment and run it:
-<code>$ module load BUSCO/4.0.6</code>+<code>$ module load BUSCO/5.2.2</code>
  
 After loading the module, consult the built-in help: After loading the module, consult the built-in help:
  
 <code>$ busco -h</code> <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: 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:
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 <code>$ cd /tmp <code>$ cd /tmp
-git clone https://gitlab.com/ezlab/busco.git +wget https://gitlab.com/ezlab/busco/-/archive/5.2.2/busco-5.2.2.tar.gz 
-cd busco +tar xf busco-5.2.2.tar.gz  
-git checkout 4.0.6 +cd busco-5.2.2 
-$ sudo mkdir /export/apps/BUSCO/4.0.6 +$ sudo mkdir /export/apps/BUSCO/5.2.2 
-$ sudo chown aorth /export/apps/BUSCO/4.0.6 +$ sudo chown aorth /export/apps/BUSCO/5.2.2 
-$ python3 -m venv /export/apps/BUSCO/4.0.6 +$ python3 -m venv /export/apps/BUSCO/5.2.2 
-$ source /export/apps/BUSCO/4.0.6/bin/activate+$ source /export/apps/BUSCO/5.2.2/bin/activate
 $ pip install --upgrade setuptools pip $ pip install --upgrade setuptools pip
 +$ pip install pandas biopython
 $ python setup.py install $ python setup.py install
-$ module load R/3.6 +$ sudo cp scripts/generate_plot.py /export/apps/BUSCO/5.2.2/bin 
-$ mkdir /export/apps/BUSCO/4.0.6/r-libs +$ module load R/4.0 
-export R_LIBS=/export/apps/BUSCO/4.0.6/r-libs +$ mkdir /export/apps/BUSCO/5.2.2/r-libs 
-Rscript -e 'install.packages("ggplot2", repos="https://cran.rstudio.com")' +$ R_LIBS=/export/apps/BUSCO/5.2.2/r-libs Rscript -e 'install.packages("ggplot2", repos="https://cran.rstudio.com")' 
-$ module load blast/2.2.31+ augustus/3.2.3 hmmer/3.2.1 sepp/4.3.8 prodigal/2.6.3 +$ sudo chown -R root:root /export/apps/BUSCO/5.2.2</code>
-$ ./scripts/busco_configurator.py config/config.ini config/myconfig.ini +
-$ sudo cp config/myconfig.ini  /export/apps/BUSCO/4.0.6/ +
-$ sudo chown -R root:root /export/apps/BUSCO/4.0.6</code> +
- +
-Consult the [[https://busco.ezlab.org/busco_userguide.html|BUSCO user guide]] for more installation and usage tips.+
busco-software.1589298357.txt.gz · Last modified: 2020/05/12 15:45 by aorth