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presto-software [2017/05/30 23:32]
aorth
presto-software [2017/05/31 00:20] (current)
aorth
Line 1: Line 1:
 ====== pRESTO ====== ====== pRESTO ======
- 
 pRESTO is a toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires. pRESTO is a toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires.
  
 ===== Information ===== ===== Information =====
  
-  * Version: 0.5.2+  * Version: 0.5.3
   * Added: June, 2016   * Added: June, 2016
-  * Link: http://​presto.readthedocs.io/​en/​latest/​index.html+  ​* Updated: May, 2017 
 +  ​* Link: http://​presto.readthedocs.io
  
 ===== Usage ===== ===== Usage =====
Line 14: Line 14:
 <​code>​$ module avail presto</​code>​ <​code>​$ module avail presto</​code>​
  
-Load presto +Load a version of presto ​into your environment:​ 
-<​code>​$ module load presto/0.5.2</​code>​+<​code>​$ module load presto/0.5.3</​code>​
  
 ===== Installation ====== ===== Installation ======
Line 21: Line 21:
 Notes from the sysadmin during installation:​ Notes from the sysadmin during installation:​
  
-<​code>​ +<​code>​$ scl enable devtoolset-2 bash
-$ cd /tmp/ +
-- install cython; a dependency of pandas; https://​pypi.python.org/​pypi/​Cython/​ +
-$ wget "​https://​pypi.python.org/​packages/​b1/​51/​bd5ef7dff3ae02a2c6047aa18d3d06df2fb8a40b00e938e7ea2f75544cac/​Cython-0.24.tar.gz#​md5=14fbc970f4a856845e633cbc09e61048"​ -O Cython-0.24.tar.gz +
-$ module load python/​3.4.3 +
-$ sudo chown -R joguya:​joguya /​export/​apps/​python/​3.4.3/​ +
- +
-- install pandas—a python3(dependency of presto) library that provides high performance easy to use data structures & data analysis tools: http://​pandas.pydata.org/​ +
-$ cd /tmp +
-$ wget https://​github.com/​pydata/​pandas/​archive/​v0.18.1.tar.gz +
-$ tar -xvf v0.18.1.tar.gz +
-$ cd pandas-0.18.1/​ +
-$ scl enable devtoolset-2 bash +
-$ module load python/​3.4.3  +
-$ python setup.py install +
- +
-- finally install presto +
-$ cd /tmp/ +
-$ wget https://​bitbucket.org/​kleinstein/​presto/​downloads/​presto-0.5.2.tar.gz +
-$ tar -xvf presto-0.5.2.tar.gz +
-$ cd presto-0.5.2 +
-$ scl enable devtoolset-2 bash+
 $ module load python/​3.4.3 $ module load python/​3.4.3
-$ sudo mkdir -p /​export/​apps/​presto/​0.5.2/ +$ sudo mkdir /​export/​apps/​presto/​0.5.3 
-$ sudo chown -R joguya:​joguya ​/​export/​apps/​presto/​0.5.2/ +$ sudo chown aorth /​export/​apps/​presto/​0.5.3 
-$ python ​setup.py install ​--install-scripts=/​export/​apps/​presto/​0.5.2/bin +$ python -m venv /​export/​apps/​presto/​0.5.3 
-sudo chown -R root:​root ​/​export/​apps/​presto/​0.5.2+/​export/​apps/​presto/​0.5.3/bin/​activate 
-$ sudo chown -R root:root /​export/​apps/​python/3.4.3+$ pip install -U pip setuptools 
-</​code>​+$ pip install -U Cython 
 +$ pip install -U numpy scipy pandas biopython 
 +$ pip install presto 
 +$ sudo chown -R root:root /​export/​apps/​presto/0.5.3</​code>​
presto-software.txt · Last modified: 2017/05/31 00:20 by aorth