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tophat-software [2014/10/17 08:22]
joguya created
tophat-software [2015/07/23 09:33]
joguya [Installation]
Line 3: Line 3:
   * Link: http://ccb.jhu.edu/software/tophat/   * Link: http://ccb.jhu.edu/software/tophat/
  
 +===== v2.0.11 =====
 +  * Version: 2.0.11
 +  * Link: http://ccb.jhu.edu/software/tophat/index.shtml
 +
 +==== Usage ====
 +  * show available versions: <code>$ module avail tophat2
 +
 +---------------------------------------------------------------------------------------------- /etc/modulefiles/ilri ----------------------------------------------------------------------------------------------
 +tophat2/2.0.11 tophat2/2.0.13 tophat2/2.0.3  tophat2/2.0.8b
 +</code>
 +  * load v2.0.13:<code>$ module load tophat2/2.0.11</code>
 +  * show help info:<code>$ tophat2 --help</code>
 +
 +===== v2.0.13 =====
 +  * Version: 2.0.13
 +  * Added: October, 2014
 +  * Link: http://ccb.jhu.edu/software/tophat/index.shtml
 +  * Changelog:
 +     * removed SAMtools as an external dependency in order to avoid incompatibility issues with recent and future changes of SAMtools and its code library (an older, stable SAMtools version is now packaged with TopHat)
 +     * fixed a few code compatibility issues when compiling on OSX 10.9
  
-===== 2.0.13 ===== 
 ==== Usage ==== ==== Usage ====
   * show available versions: <code>$ module avail tophat2   * show available versions: <code>$ module avail tophat2
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 > **NOTE** > **NOTE**
 > Older versions of tophat2 required SAMtools to be loaded/present, unlike this new version which comes with its own SAMtools inorder to avoid incompatibility issues. > Older versions of tophat2 required SAMtools to be loaded/present, unlike this new version which comes with its own SAMtools inorder to avoid incompatibility issues.
 +
   * <code>wget http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.13.Linux_x86_64.tar.gz   * <code>wget http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.13.Linux_x86_64.tar.gz
 tar -xvf tophat-2.0.13.Linux_x86_64.tar.gz tar -xvf tophat-2.0.13.Linux_x86_64.tar.gz
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   * deploy using ansible<code>ansible-playbook compute.yml --limit=compute --tags=modules -K</code>   * deploy using ansible<code>ansible-playbook compute.yml --limit=compute --tags=modules -K</code>
  
 +===== v2.1.0 =====
 +  * Version: 2.1.0
 +  * Added: July, 2015
 +  * Link: http://ccb.jhu.edu/software/tophat/index.shtml
 +
 +=== Installation ===
 +  * Tophat2 is already compiled, just download the tarball & copy content to /export/apps<code>wget http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.0.Linux_x86_64.tar.gz
 +tar -xvf tophat-2.1.0.Linux_x86_64.tar.gz
 +cd tophat-2.1.0.Linux_x86_64/
 +sudo mkdir /export/apps/tophat2/2.1.0
 +sudo cp -r . /export/apps/tophat2/2.1.0/
 +</code>
  
tophat-software.txt · Last modified: 2015/07/23 09:38 by joguya