Differences

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--- flash-software [2014/12/16 07:11] – created joguya
+++ 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.
-==== v1.2.11 ====
+===== Information =====
   * Version: 1.2.11
   * 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>