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cutadapt-software [2015/06/24 12:08]
aorth
cutadapt-software [2019/01/20 13:45] (current)
aorth
Line 4: Line 4:
 ===== Information ===== ===== Information =====
  
-  * Version: ​v1.8.1+  * Version: ​1.18
   * Added: June, 2015   * Added: June, 2015
 +  * Updated: January, 2019
   * Link: https://​github.com/​marcelm/​cutadapt   * Link: https://​github.com/​marcelm/​cutadapt
  
 ===== Usage ===== ===== Usage =====
  
-=== See versions of cutadapt ​which are available === +See available ​versions of cutadapt: 
-<​code>​module avail cutadapt</​code>​+<​code>​module avail cutadapt</​code>​ 
 + 
 +Load one version into your environment and run it: 
 +<​code>​$ module load cutadapt/​1.18 
 +cutadapt</​code>​
  
 ===== Installation ====== ===== Installation ======
 Notes from the sysadmin during installation:​ Notes from the sysadmin during installation:​
  
-<​code>​$ sudo mkdir -p /​export/​apps/​cutadapt/​v1.8.1 +<​code>​$ sudo mkdir -p /​export/​apps/​cutadapt/​1.18 
-$ module load python/2.7.8 +$ sudo chown aorth /​export/​apps/​cutadapt/​1.18 
-$ sudo chown aorth /​export/​apps/​cutadapt/​v1.8.1 +python36 ​-m venv /​export/​apps/​cutadapt/​1.18 
-pip install cutadapt ​--install-option="​--prefix=/​export/​apps/​cutadapt/​v1.8.1" +/​export/​apps/​cutadapt/​1.18/​bin/​activate 
-$ sudo chown root:root /​export/​apps/​cutadapt/​v1.8.1</​code>​+$ pip install --upgrade pip setuptools 
 +$ pip install cutadapt==v1.18 
 +$ sudo chown -R root:root /​export/​apps/​cutadapt/​1.18</​code>​ 
 + 
 +Installation is greatly simplified by using Python 3's built-in venv module to create a dedicated environment,​ then use standard pip to install cutadapt and its dependencies.
cutadapt-software.1435136913.txt.gz · Last modified: 2015/06/24 12:08 by aorth