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--- software:alignment:tophat:2.0.3 [2012/06/13 08:37] – aorth
+++ software:alignment:tophat:2.0.3 [2012/06/13 08:41] (current) – [Prepare module file] aorth
@@ Line 16: / Line 16: @@
 Create the module file, ///export/apps/modules/modulefiles/tophat/2.0.3//:
-<file>#%Module1.0
+<file>
+#%Module1.0
 #####################################################################
 ##
-## cufflinks Modulefile
+## tophat Modulefile
-## by Alan Orth, a.orth@cgiar.org
+## by Alan Orth, <a.orth@cgiar.org>
+## June 13, 2012
 ##
 set version   2.0.3
-set prefix    /export/apps/cufflinks/${version}
+set appname   tophat
-set exec_prefix   ${prefix}
+set prefix    /export/apps/${appname}/${version}
-set url "http://cufflinks.cbcb.umd.edu/"
+set exec_prefix   ${prefix}/bin
-set msg "This module adds cufflinks v$version to various paths\n\ncufflinks Official Site: $url\n"
+set datarootdir   ${prefix}/share
+set url "http://tophat.cbcb.umd.edu"
+set msg "This module adds tophat v$version to various paths\n\ntophat Official Site: $url\n"
 proc ModulesHelp { } {
@@ Line 34: / Line 38: @@
 module-whatis   "$msg"
-conflict      cufflinks
+conflict tophat
-prepend-path  PATH    ${exec_prefix}/bin
+prepend-path  PATH    ${exec_prefix}
-# cufflinks 1.0.3 was compiled against boost 1.47.0, make sure if can find boost!
+prepend-path  MANPATH   ${datarootdir}/man
-prepend-path  LD_LIBRARY_PATH /export/apps/boost/1.47.0/lib
-# cufflinks depends on samtools, load the samtools module as well
+# tophat depends on samtools, load the samtools module as well
 if { ![is-loaded samtools] } {
     module load samtools
+}
+# tophat depends on bowtie, load the bowtie module as well
+if { ![is-loaded bowtie] } {
+    module load bowtie
 }</file>
 ==== Test module file ====
-<code>module load cufflinks/2.0.0</code>
+<code>module load tophat/2.0.3</code>