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cd-hit-software [2016/08/30 07:13] – created joguyacd-hit-software [2021/03/17 13:19] (current) aorth
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 ====== CD-HIT ====== ====== CD-HIT ======
- 
 A program for clustering and comparing protein or nucleotide sequences. A program for clustering and comparing protein or nucleotide sequences.
  
 ===== Information ===== ===== Information =====
  
-  * Version: 4.6.6+  * Version: 4.8.1
   * Added: August, 2016   * Added: August, 2016
-  * Link: http://weizhongli-lab.org/cd-hit/+  * Updated: March, 2021 
 +  * Link: https://github.com/weizhongli/cdhit
  
 ===== Usage ===== ===== Usage =====
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 <code>$ module avail cd-hit</code> <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.
 +$ cd-hit</code>
  
 ===== Installation ====== ===== Installation ======
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 Notes from the sysadmin during installation: 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.+
-$ sudo mkdir -p /export/apps/cd-hit/4.6.6/ +
-sudo chown joguya:joguya /export/apps/cd-hit/4.6.6/+
 $ make $ make
-sed -i 's|#!/usr/bin/perl|#!/usr/bin/env perl|g' *.pl +sudo mkdir -/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> +
cd-hit-software.txt · Last modified: 2021/03/17 13:19 by aorth