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--- cutadapt-software [2015/06/24 09:08]
aorth created
+++ cutadapt-software [2019/01/20 10:45]
aorth
@@ Line 1: / Line 1: @@
 ====== cutadapt ======
-A framework to process and analyze data from high-throughput sequencing (HTS) assays.
+Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
 ===== Information =====
-  * Version: v1.8.1
+  * Version: 1.18
   * Added: June, 2015
+  * Updated: January, 2019
   * Link: https://github.com/marcelm/cutadapt
 ===== 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 ======
 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, etc to install cutadapt and its dependencies.

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