From b3fe96513c5243194d8b1011cac8e8514f2736d5 Mon Sep 17 00:00:00 2001
From: Per Unneberg <per.unneberg@scilifelab.se>
Date: Fri, 15 Jun 2012 10:44:39 +0200
Subject: [PATCH] Add igvtools 2.1.7 and snpEff 2.1b

---
 ucsc_tools/4 => igvtools/2.1.7 | 12 ++++++------
 snpEff/2.1b                    | 36 ++++++++++++++++++++++++++++++++++
 2 files changed, 42 insertions(+), 6 deletions(-)
 rename ucsc_tools/4 => igvtools/2.1.7 (62%)
 create mode 100644 snpEff/2.1b

diff --git a/ucsc_tools/4 b/igvtools/2.1.7
similarity index 62%
rename from ucsc_tools/4
rename to igvtools/2.1.7
index 47779f1..f631572 100644
--- a/ucsc_tools/4
+++ b/igvtools/2.1.7
@@ -1,6 +1,6 @@
 #%Module1.0#####################################################################
 ##
-## ucsc_tools modulefile
+## CRISP modulefile
 ##
 
 source $env(MODULE_INCLUDE)/functions.tcl
@@ -9,19 +9,19 @@ getCluster
 set components [ file split [ module-info name ] ]
 set version [ lindex $components 1 ]
 
-set     modroot         /proj/a2010002/nobackup/sw/mf/bioinfo-tools/misc/ucsc_tools/20120530/bin
+set     modroot          /proj/a2010002/nobackup/sw/mf/bioinfo-tools/igvtools/2.1.7/IGVTools
 
 proc ModulesHelp { } {
         global version modroot
 
-        puts stderr "\tucsc_tools - use ucsc_tools $version"
+        puts stderr "\tigvtools - use igvtools $version"
         puts stderr "\n\tVersion $version\n"
 }
 
-module-whatis   "Loads ucsc_tools environment."
+module-whatis   "Loads igvtools environment."
 
 # Only one version at a time
-conflict ucsc_tools
+conflict igvtools
 
 #Log loading to syslog
 logToSyslog
@@ -32,4 +32,4 @@ prepend-path    PATH            $modroot
 
 # Environments for the program:
 #
-setenv               UCSCTOOLS_HOME      $modroot
+setenv               IGVTOOLS_HOME      $modroot
diff --git a/snpEff/2.1b b/snpEff/2.1b
new file mode 100644
index 0000000..d641986
--- /dev/null
+++ b/snpEff/2.1b
@@ -0,0 +1,36 @@
+#%Module1.0#####################################################################
+##
+## snpEff modulefile
+##
+
+source $env(MODULE_INCLUDE)/functions.tcl
+getCluster
+
+set components [ file split [ module-info name ] ]
+set version [ lindex $components 1 ]
+
+set     modroot          /proj/a2010002/nobackup/sw/mf/bioinfo-tools/snpEff/snpEff_2_1b
+
+proc ModulesHelp { } {
+        global version modroot
+
+        puts stderr "\tsnpEff - use snpEff $version"
+        puts stderr "\n\tVersion $version\n"
+}
+
+module-whatis   "Loads snpEff environment."
+
+# Only one version at a time
+conflict snpEff
+
+#Log loading to syslog
+logToSyslog
+
+# Directories for the program:
+#
+prepend-path    PATH            $modroot
+prepend-path    CLASSPATH       $modroot
+
+# Environments for the program:
+#
+setenv               SNPEFF_HOME      $modroot