Differences

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--- presto-software [2016/06/28 13:20] – created joguya
+++ presto-software [2020/03/15 11:54] (current) – aorth
@@ Line 1: / Line 1: @@
 ====== pRESTO ======
 pRESTO is a toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires.
 ===== Information =====
-  * Version: 0.5.2
+  * Version: 0.5.13
   * Added: June, 2016
-  * Link: http://presto.readthedocs.io/en/latest/index.html
+  * Updated: March, 2020
+  * Link: https://presto.readthedocs.io
 ===== Usage =====
@@ Line 14: / Line 14: @@
 <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/0.5.13</code>
 ===== Installation ======
@@ Line 21: / Line 21: @@
 Notes from the sysadmin during installation:
-<code>
+<code>$ scl enable devtoolset-7 bash
-$ cd /tmp/
+$ sudo mkdir -p /export/apps/presto/0.5.13
-- install cython; a dependency of pandas; https://pypi.python.org/pypi/Cython/
+$ sudo chown aorth /export/apps/presto/0.5.13
-$ cd /tmp/
+$ python3.6m -m venv /export/apps/presto/0.5.13
-$ wget "https://pypi.python.org/packages/b1/51/bd5ef7dff3ae02a2c6047aa18d3d06df2fb8a40b00e938e7ea2f75544cac/Cython-0.24.tar.gz#md5=14fbc970f4a856845e633cbc09e61048" -O Cython-0.24.tar.gz
+$ source /export/apps/presto/0.5.13/bin/activate
-$ module load python/3.4.3
+$ pip install --upgrade setuptools pip
-$ sudo chown -R joguya:joguya /export/apps/python/3.4.3/
+$ pip install presto
+$ sudo chown -R root:root /export/apps/presto/0.5.13</code>
-- 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
-$ sudo mkdir -p /export/apps/presto/0.5.2/
-$ sudo chown -R joguya:joguya /export/apps/presto/0.5.2/
-$ python setup.py install --install-scripts=/export/apps/presto/0.5.2/bin
-$ sudo chown -R root:root /export/apps/presto/0.5.2/
-</code>