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presto-software
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presto-software [2017/05/30 23:32] aorth |
presto-software [2017/05/31 00:20] (current) aorth |
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| ====== 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
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