From e8e47aedba1d83c6ded9d8db9d8967524587e83e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 7 Feb 2018 16:16:15 +0100
Subject: [PATCH] module cleanup in new lua version
---
modulefiles/SAMtools/1.5 | 13 ++++++-------
modulefiles/SRAtoolkit/2.8.2 | 10 ++++++----
2 files changed, 12 insertions(+), 11 deletions(-)
diff --git a/modulefiles/SAMtools/1.5 b/modulefiles/SAMtools/1.5
index d5c4295..2d13e9f 100644
--- a/modulefiles/SAMtools/1.5
+++ b/modulefiles/SAMtools/1.5
@@ -32,11 +32,10 @@
# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL license and that you accept its terms.
-setenv("LAST_MODULE","SAMtools/1.5")
-whatis([===[loads SAMtools 1.5 (Debian 9) environment ]===])
+local root = "/Xnfs/site/lbmcdb/common/modules/apps/SAMtools/1.5/"
+
conflict("SAMtools")
-prepend_path{"PATH","/Xnfs/site/lbmcdb/common/modules/apps/SAMtools/1.5/bin",delim=":",priority="0"}
-prepend_path{"LD_LIBRARY_PATH","/Xnfs/site/lbmcdb/common/modules/apps/SAMtools/1.5/lib",delim=":",priority="0"}
-prepend_path{"INCLUDE","/Xnfs/site/lbmcdb/common/modules/apps/SAMtools/1.5/include/htslib",delim=":",priority="0"}
-prepend_path{"MANPATH","/Xnfs/site/lbmcdb/common/modules/apps/SAMtools/1.5/share/man",delim=":",priority="0"}
-setenv("SAMTOOLS_PATH","/Xnfs/site/lbmcdb/common/modules/apps/SAMtools/1.5/bin")
+
+whatis([===[loads SAMtools 1.5 (Debian 9) environment ]===])
+prepend_path{"PATH", pathJoin(root, "bin")}
+setenv("SRATOOLKIT_PATH", pathJoin(root, "bin"))
diff --git a/modulefiles/SRAtoolkit/2.8.2 b/modulefiles/SRAtoolkit/2.8.2
index 2a0641d..faa0745 100644
--- a/modulefiles/SRAtoolkit/2.8.2
+++ b/modulefiles/SRAtoolkit/2.8.2
@@ -32,8 +32,10 @@
# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL license and that you accept its terms.
-setenv("LAST_MODULE","SRAtoolkit/2.8.2")
-whatis([===[loads SRAtoolkit 2.8.2 (Debian 7) environment ]===])
+local root = "/Xnfs/site/lbmcdb/common/modules/apps/SRAtoolkit/2.8.2/"
+
conflict("SRAtoolkit")
-prepend_path{"PATH","/Xnfs/site/lbmcdb/common/modules/apps/SRAtoolkit/2.8.2/bin/",delim=":",priority="0"}
-setenv("SRATOOLKIT_PATH","/Xnfs/site/lbmcdb/common/modules/apps/SRAtoolkit/2.8.2/bin/")
+
+whatis([===[loads SRAtoolkit 2.8.2 (Debian 7) environment ]===])
+prepend_path{"PATH", pathJoin(root, "bin")}
+setenv("SRATOOLKIT_PATH", pathJoin(root, "bin"))
--
GitLab