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pasta-software [2018/10/21 15:51]
aorth created
pasta-software [2018/10/21 16:01] (current)
aorth
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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 pasta/​git-d939adb2 <​code>​$ module load pasta/​git-d939adb2
-$ run_pasta.py -h</​code>​+$ run_pasta.py -i input_fasta [-t starting_tree]</​code>​
  
 Consult the [[https://​github.com/​smirarab/​pasta/​blob/​master/​pasta-doc/​pasta-tutorial.md|Pasta tutorial]] for more information. Consult the [[https://​github.com/​smirarab/​pasta/​blob/​master/​pasta-doc/​pasta-tutorial.md|Pasta tutorial]] for more information.
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 Notes from the sysadmin during installation:​ Notes from the sysadmin during installation:​
  
-<​code></​code>​+<​code>​$ cd /tmp 
 +$ mkdir pasta-code 
 +$ cd pasta-code 
 +$ git clone https://​github.com/​smirarab/​pasta.git 
 +$ git clone https://​github.com/​smirarab/​sate-tools-linux.git 
 +$ git clone https://​github.com/​kodicollins/​pasta-databases sate-tools-linux/​pasta-databases 
 +$ cd pasta 
 +$ sudo mkdir -p /​export/​apps/​pasta/​git-d939adb2/​lib/​python2.7/​site-packages 
 +$ sudo chown -R aorth /​export/​apps/​pasta/​git-d939adb2 
 +$ export PYTHONPATH=/​export/​apps/​pasta/​git-d939adb2/​lib/​python2.7/​site-packages 
 +$ python setup.py develop --prefix=/​export/​apps/​pasta/​git-d939adb2 
 +$ cd .. 
 +$ sudo cp -r sate-tools-linux/​ /​export/​apps/​pasta/​git-d939adb2 
 +$ sudo chown -R root:root /​export/​apps/​pasta/​git-d939adb2 
 +# for graphical interface (use on HPC only to avoid installing stupid dependencies on nodes) 
 +$ sudo yum install wxPython.x86_64</​code>​
  
 Note that the Pasta project does not tag their releases, so I've used the git commit hash at the time of installation. Note that the Pasta project does not tag their releases, so I've used the git commit hash at the time of installation.
pasta-software.txt · Last modified: 2018/10/21 16:01 by aorth