Differences

This shows you the differences between two versions of the page.

--- cd-hit-software [2016/08/30 07:13] – created joguya
+++ cd-hit-software [2021/03/17 13:19] (current) – aorth
@@ Line 1: / Line 1: @@
 ====== CD-HIT ======
 A program for clustering and comparing protein or nucleotide sequences.
 ===== Information =====
-  * Version: 4.6.6
+  * Version: 4.8.1
   * Added: August, 2016
-  * Link: http://weizhongli-lab.org/cd-hit/
+  * Updated: March, 2021
+  * Link: https://github.com/weizhongli/cdhit
 ===== Usage =====
@@ Line 14: / Line 14: @@
 <code>$ module avail cd-hit</code>
-Load cd-hit
+Load one version into your environment and run it:
-<code>$ module load cd-hit/4.6.6</code>
+<code>$ module load cd-hit/4.8.1
+$ cd-hit</code>
 ===== Installation ======
@@ Line 21: / Line 22: @@
 Notes from the sysadmin during installation:
-<code>
+<code>$ cd /tmp
-$ cd /tmp
+$ wget https://github.com/weizhongli/cdhit/releases/download/V4.8.1/cd-hit-v4.8.1-2019-0228.tar.gz
-$ wget -qO - https://github.com/weizhongli/cdhit/archive/V4.6.6.tar.gz | tar -xzv
+$ tar xf cd-hit-v4.8.1-2019-0228.tar.gz
-$ cd cdhit-4.6.6/
+$ cd cd-hit-v4.8.1-2019-0228
-$ scl enable devtoolset-2 bash
-$ module load openmpi/1.8.2
-$ sudo mkdir -p /export/apps/cd-hit/4.6.6/
-$ sudo chown joguya:joguya /export/apps/cd-hit/4.6.6/
 $ make
-$ sed -i 's|#!/usr/bin/perl|#!/usr/bin/env perl|g' *.pl
+$ sudo mkdir -p /export/apps/cd-hit/4.8.1
-$ find . -type f -perm /o+x -exec cp -v {} /export/apps/cd-hit/4.6.6/ \;
+$ sudo chown aorth /export/apps/cd-hit/4.8.1
-$ cd cd-hit-auxtools
+$ PREFIX=/export/apps/cd-hit/4.8.1 make install
-$ make
+$ sudo chown -R root:root /export/apps/cd-hit/4.8.1</code>
-$ sed -i 's|#!/usr/bin/perl|#!/usr/bin/env perl|g' *.pl
-$ find . -type f -perm /o+x -exec cp -v {} /export/apps/cd-hit/4.6.6/ \;
-$ sudo chown -R root:root /export/apps/cd-hit/4.6.6/</code>