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flash-software [2014/12/16 07:11]
joguya created
flash-software [2017/09/20 13:29] (current)
aorth
Line 2: Line 2:
 FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast tool to merge paired-end reads from fragments that are shorter than twice the length of reads. The extended length of reads has a significant positive impact on improvement of genome assemblies. FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast tool to merge paired-end reads from fragments that are shorter than twice the length of reads. The extended length of reads has a significant positive impact on improvement of genome assemblies.
  
-==== v1.2.11 ====+===== Information =====
   * Version: 1.2.11   * Version: 1.2.11
   * Added: December, 2014   * Added: December, 2014
-  * Link: http://sourceforge.net/projects/flashpage/+  * Link: http://sourceforge.net/projects/flashpage
  
-=== Usage === +===== Usage ===== 
-  Show all available versions of flash<code>module avail flash</code> +Show all available versions of flash:
-  * Load flash module<code>module load flash/1.2.11</code> +
-  * get quick help:<code>flash --help</code>+
  
 +<code>$ module avail flash</code>
  
-=== Installation === +Load flash into your environment:
-  * Download flash src tarball, extract it & compile it<code>wget "http://downloads.sourceforge.net/project/flashpage/FLASH-1.2.11.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fflashpage%2F&ts=1418712841&use_mirror=tenet" -O FLASH-1.2.11.tar.gz +
-tar -xvf FLASH-1.2.11.tar.gz +
-cd FLASH-1.2.11 +
-make +
-sudo mkdir -p /export/apps/FLASH/1.2.11 +
-sudo cp flash /export/apps/FLASH/1.2.11/</code> +
-  * flash module file<code> +
-#%Module1.0 +
-##################################################################### +
-## +
-## FLASH Modulefile +
-## By James Oguya, j.oguya@cgiar.org +
-## December, 2014 +
-##+
  
-set appname         FLASH +<code>$ module load flash/1.2.11</code>
-set version         1.2.11 +
-set prefix          /export/apps/${appname}/${version} +
-set exec_prefix     ${prefix} +
-set url "http://sourceforge.net/projects/flashpage/" +
-set msg "FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast tool to merge paired-end reads from fragments that are shorter than twice the length of reads. The extended length of reads has a significant positive impact on improvement of genome assemblies..\nFLASH Official Site: $url\n"+
  
-module-whatis $msg+Get quick help: 
 +<code>flash --help</code>
  
-proc ModulesHelp { } { +===== Installation ===== 
-    puts stderr "$msg" +Notes from the sysadmin during installation.
-+
- +
-conflict        FLASH +
- +
-prepend-path    PATH    ${exec_prefix} +
-</code> +
- +
-  * deploy the new module using ansible<code>ansible-playbook site.yml -u joguya -K -s --limit=compute --tags=module</code>+
  
 +<code>$ wget "http://downloads.sourceforge.net/project/flashpage/FLASH-1.2.11.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fflashpage%2F&ts=1418712841&use_mirror=tenet" -O FLASH-1.2.11.tar.gz
 +$ tar -xvf FLASH-1.2.11.tar.gz
 +$ cd FLASH-1.2.11
 +$ make
 +$ sudo mkdir -p /export/apps/FLASH/1.2.11
 +$ sudo cp flash /export/apps/FLASH/1.2.11</code>
flash-software.1418713867.txt.gz · Last modified: 2014/12/16 07:11 by joguya