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busco-software [2017/09/11 13:06]
aorth 		busco-software [2020/05/12 15:45]
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 ===== Information ===== ===== Information =====
  
-  * Latest Version: 3.0.2+  * Latest Version: 4.0.6
   * Added: August, 2015   * Added: August, 2015
-  * Updated: September, 2017 +  * Updated: May, 2020 
-  * Link: http://busco.ezlab.org+  * Link: https://busco.ezlab.org
  
 ===== Usage ===== ===== Usage =====
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 <code>$ module avail BUSCO</code> <code>$ module avail BUSCO</code>
  
-Load one version into your environment: +Load one version into your environment and run it: 
-<code>$ module load BUSCO/3.0.2</code>+<code>$ module load BUSCO/4.0.6</code>
  
 After loading the module, consult the built-in help: After loading the module, consult the built-in help:
  
-<code>$ run_BUSCO.py -h</code>+<code>$ busco -h</code>
  
 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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 $ git clone https://gitlab.com/ezlab/busco.git $ git clone https://gitlab.com/ezlab/busco.git
 $ cd busco $ cd busco
-$ git checkout 3.0.2 +$ git checkout 4.0.6 
-$ module load python/3.6.1 +$ sudo mkdir /export/apps/BUSCO/4.0.6 
-$ sudo mkdir /export/apps/BUSCO/3.0.2 +$ sudo chown aorth /export/apps/BUSCO/4.0.6 
-$ sudo chown aorth /export/apps/BUSCO/3.0.2 +$ python3 -m venv /export/apps/BUSCO/4.0.6 
-$ python -m venv /export/apps/BUSCO/3.0.2 +$ source /export/apps/BUSCO/4.0.6/bin/activate 
-$ . /export/apps/BUSCO/3.0.2/bin/activate+$ pip install --upgrade setuptools pip
 $ python setup.py install $ python setup.py install
-$ cp -rv * /export/apps/BUSCO/3.0.2 +$ module load R/3.6 
-$ cp /export/apps/BUSCO/3.0.2/config/config.ini.default /export/apps/BUSCO/3.0.2/config/config.ini +$ mkdir /export/apps/BUSCO/4.0.6/r-libs 
-# edit paths in /export/apps/BUSCO/3.0.2/config/config.ini +$ export R_LIBS=/export/apps/BUSCO/4.0.6/r-libs 
-$ sudo chown -R root:root /export/apps/BUSCO/3.0.2</code>+$ 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 
 +$ ./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.txt · Last modified: 2020/05/12 15:45 by aorth

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