From 8ec143033a97c787e46c3a6d1a5ad84d0e0f5065 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 5 Mar 2019 15:50:06 +0100
Subject: [PATCH] changes path to lowercase in .lua
---
modulefiles/{gcc => GCC}/4.9.4.lua | 0
modulefiles/{gcc => GCC}/5.4.0.lua | 0
modulefiles/{gcc => GCC}/6.4.0.lua | 0
modulefiles/{gcc => GCC}/7.2.0.lua | 0
modulefiles/{gcc => GCC}/default | 0
modulefiles/{java => Java}/1.7.0_21.lua | 0
modulefiles/{java => Java}/1.7.0_71.lua | 0
modulefiles/{java => Java}/1.8.0_151.lua | 0
modulefiles/{python => Python}/2.7.13.lua | 0
modulefiles/{python => Python}/3.6.1.lua | 0
modulefiles/{r => R}/3.2.4.lua | 0
modulefiles/{r => R}/3.4.3.lua | 0
modulefiles/bcftools/1.7.lua | 8 +--
modulefiles/bedtools/2.25.0.lua | 6 +--
modulefiles/bowtie2/2.3.2.lua | 6 +--
modulefiles/bowtie2/2.3.4.1.lua | 6 +--
modulefiles/cdhit/4.6.8 | 64 -----------------------
modulefiles/cdhit/4.6.8.lua | 44 ++++++++++++++++
modulefiles/deeptools/3.0.2.lua | 4 +-
modulefiles/fastqc/0.11.5.lua | 6 +--
modulefiles/gatk/4.0.10.1.lua | 8 +--
modulefiles/htseq/0.8.0.lua | 4 +-
modulefiles/htseq/0.9.1.lua | 4 +-
modulefiles/rsem/1.3.0.lua | 8 +--
modulefiles/rsem/1.3.1.lua | 8 +--
modulefiles/salmon/0.8.2.lua | 8 +--
modulefiles/samtools/1.5.lua | 8 +--
modulefiles/samtools/1.7.lua | 8 +--
modulefiles/sratoolkit/2.8.2.lua | 6 +--
modulefiles/tophat/2.1.1.lua | 2 +-
modulefiles/trimmomatic/0.37.lua | 8 +--
modulefiles/urqt/d62c1f8.lua | 8 +--
32 files changed, 102 insertions(+), 122 deletions(-)
rename modulefiles/{gcc => GCC}/4.9.4.lua (100%)
rename modulefiles/{gcc => GCC}/5.4.0.lua (100%)
rename modulefiles/{gcc => GCC}/6.4.0.lua (100%)
rename modulefiles/{gcc => GCC}/7.2.0.lua (100%)
rename modulefiles/{gcc => GCC}/default (100%)
rename modulefiles/{java => Java}/1.7.0_21.lua (100%)
rename modulefiles/{java => Java}/1.7.0_71.lua (100%)
rename modulefiles/{java => Java}/1.8.0_151.lua (100%)
rename modulefiles/{python => Python}/2.7.13.lua (100%)
rename modulefiles/{python => Python}/3.6.1.lua (100%)
rename modulefiles/{r => R}/3.2.4.lua (100%)
rename modulefiles/{r => R}/3.4.3.lua (100%)
delete mode 100644 modulefiles/cdhit/4.6.8
create mode 100644 modulefiles/cdhit/4.6.8.lua
diff --git a/modulefiles/gcc/4.9.4.lua b/modulefiles/GCC/4.9.4.lua
similarity index 100%
rename from modulefiles/gcc/4.9.4.lua
rename to modulefiles/GCC/4.9.4.lua
diff --git a/modulefiles/gcc/5.4.0.lua b/modulefiles/GCC/5.4.0.lua
similarity index 100%
rename from modulefiles/gcc/5.4.0.lua
rename to modulefiles/GCC/5.4.0.lua
diff --git a/modulefiles/gcc/6.4.0.lua b/modulefiles/GCC/6.4.0.lua
similarity index 100%
rename from modulefiles/gcc/6.4.0.lua
rename to modulefiles/GCC/6.4.0.lua
diff --git a/modulefiles/gcc/7.2.0.lua b/modulefiles/GCC/7.2.0.lua
similarity index 100%
rename from modulefiles/gcc/7.2.0.lua
rename to modulefiles/GCC/7.2.0.lua
diff --git a/modulefiles/gcc/default b/modulefiles/GCC/default
similarity index 100%
rename from modulefiles/gcc/default
rename to modulefiles/GCC/default
diff --git a/modulefiles/java/1.7.0_21.lua b/modulefiles/Java/1.7.0_21.lua
similarity index 100%
rename from modulefiles/java/1.7.0_21.lua
rename to modulefiles/Java/1.7.0_21.lua
diff --git a/modulefiles/java/1.7.0_71.lua b/modulefiles/Java/1.7.0_71.lua
similarity index 100%
rename from modulefiles/java/1.7.0_71.lua
rename to modulefiles/Java/1.7.0_71.lua
diff --git a/modulefiles/java/1.8.0_151.lua b/modulefiles/Java/1.8.0_151.lua
similarity index 100%
rename from modulefiles/java/1.8.0_151.lua
rename to modulefiles/Java/1.8.0_151.lua
diff --git a/modulefiles/python/2.7.13.lua b/modulefiles/Python/2.7.13.lua
similarity index 100%
rename from modulefiles/python/2.7.13.lua
rename to modulefiles/Python/2.7.13.lua
diff --git a/modulefiles/python/3.6.1.lua b/modulefiles/Python/3.6.1.lua
similarity index 100%
rename from modulefiles/python/3.6.1.lua
rename to modulefiles/Python/3.6.1.lua
diff --git a/modulefiles/r/3.2.4.lua b/modulefiles/R/3.2.4.lua
similarity index 100%
rename from modulefiles/r/3.2.4.lua
rename to modulefiles/R/3.2.4.lua
diff --git a/modulefiles/r/3.4.3.lua b/modulefiles/R/3.4.3.lua
similarity index 100%
rename from modulefiles/r/3.4.3.lua
rename to modulefiles/R/3.4.3.lua
diff --git a/modulefiles/bcftools/1.7.lua b/modulefiles/bcftools/1.7.lua
index a25b615..66886f2 100644
--- a/modulefiles/bcftools/1.7.lua
+++ b/modulefiles/bcftools/1.7.lua
@@ -34,10 +34,10 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
--]=====]
-local root = "/Xnfs/lbmcdb/common/modules/apps/BCFtools/1.7/"
+local root = "/Xnfs/lbmcdb/common/modules/apps/bcftools/1.7/"
-conflict("BCFtools")
+conflict("bcftools")
-whatis([===[loads BCFtools 1.7 (Debian 9) environment ]===])
+whatis([===[loads bcftools 1.7 (Debian 9) environment ]===])
prepend_path{"PATH", pathJoin(root, "bin")}
-setenv("SRATOOLKIT_PATH", pathJoin(root, "bin"))
+setenv("BCFTOOLS_PATH", pathJoin(root, "bin"))
diff --git a/modulefiles/bedtools/2.25.0.lua b/modulefiles/bedtools/2.25.0.lua
index 3bb7e4e..72e6f88 100644
--- a/modulefiles/bedtools/2.25.0.lua
+++ b/modulefiles/bedtools/2.25.0.lua
@@ -34,10 +34,10 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
--]=====]
-local root = "/Xnfs/lbmcdb/common/modules/apps/BEDtools/2.25.0"
+local root = "/Xnfs/lbmcdb/common/modules/apps/bedtools/2.25.0"
-conflict("BEDtools")
+conflict("bedtools")
-whatis([===[loads BEDtools 2.25.0 (Debian 9) environment ]===])
+whatis([===[loads bedtools 2.25.0 (Debian 9) environment ]===])
prepend_path{"PATH", pathJoin(root, "bin")}
setenv("BEDTOOLS_PATH", pathJoin(root, "bin"))
diff --git a/modulefiles/bowtie2/2.3.2.lua b/modulefiles/bowtie2/2.3.2.lua
index 59c73b5..b165552 100644
--- a/modulefiles/bowtie2/2.3.2.lua
+++ b/modulefiles/bowtie2/2.3.2.lua
@@ -34,10 +34,10 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
--]=====]
-local root = "/Xnfs/lbmcdb/common/modules/apps/Bowtie2/2.3.2"
+local root = "/Xnfs/lbmcdb/common/modules/apps/bowtie2/2.3.2"
-conflict("Bowtie2")
+conflict("bowtie2")
-whatis([===[loads Bowtie2 2.3.2 (Debian 9) environment ]===])
+whatis([===[loads bowtie2 2.3.2 (Debian 9) environment ]===])
prepend_path{"PATH", pathJoin(root, "bin")}
setenv("BOWTIE2_PATH", pathJoin(root, "bin"))
diff --git a/modulefiles/bowtie2/2.3.4.1.lua b/modulefiles/bowtie2/2.3.4.1.lua
index cfdd1d1..50104b4 100644
--- a/modulefiles/bowtie2/2.3.4.1.lua
+++ b/modulefiles/bowtie2/2.3.4.1.lua
@@ -34,10 +34,10 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
--]=====]
-local root = "/Xnfs/lbmcdb/common/modules/apps/Bowtie2/2.3.4.1"
+local root = "/Xnfs/lbmcdb/common/modules/apps/bowtie2/2.3.4.1"
-conflict("Bowtie2")
+conflict("bowtie2")
-whatis([===[loads Bowtie2 2.3.4.1 (Debian 9) environment ]===])
+whatis([===[loads bowtie2 2.3.4.1 (Debian 9) environment ]===])
prepend_path{"PATH", pathJoin(root, "bin")}
setenv("BOWTIE2_PATH", pathJoin(root, "bin"))
diff --git a/modulefiles/cdhit/4.6.8 b/modulefiles/cdhit/4.6.8
deleted file mode 100644
index 8a48a7f..0000000
--- a/modulefiles/cdhit/4.6.8
+++ /dev/null
@@ -1,64 +0,0 @@
-#%Module1.0####################################################################
-# Copyright claire burny for the LBMC UMR 5239 ©.
-# contributor(s) : claire burny (2017)
-#
-# claire.burny@ens-lyon.fr
-#
-# This software is a computer program whose purpose is to manage dated file
-# names in complience with the bioinformatic good practices used in the LBMC.
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software. You can use,
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info".
-#
-# As a counterpart to the access to the source code and rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty and the software's author, the holder of the
-# economic rights, and the successive licensors have only limited
-# liability.
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading, using, modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean that it is complicated to manipulate, and that also
-# therefore means that it is reserved for developers and experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or
-# data to be ensured and, more generally, to use and operate it in the
-# same conditions as regards security.
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-##
-##
-###############################################################################
-# for Tcl script use only
-set version 4.6.8
-set modname CDHIT
-set osarch "Debian 7"
-set modroot /Xnfs/site/lbmcdb/modules/apps/CDHIT/4.6.8
-
-setenv LAST_MODULE $modname/$version
-
-###############################################################################
-proc ModulesHelp { } {
- global modname version osarch
- puts stderr "\nThis set the environment variables for $modname $version - $osarch."
-}
-
-
-module-whatis "loads $modname $version ($osarch) environment"
-###############################################################################
-
-# conflict
-conflict $modname
-
-if [ module-info mode load ] {
- prereq Base/psmn
-}
-
-prepend-path PATH $modroot/bin
-setenv CDHIT_PATH $modroot/bin
diff --git a/modulefiles/cdhit/4.6.8.lua b/modulefiles/cdhit/4.6.8.lua
new file mode 100644
index 0000000..762e845
--- /dev/null
+++ b/modulefiles/cdhit/4.6.8.lua
@@ -0,0 +1,44 @@
+--[=====[
+Copyright laurent modolo for the LBMC UMR 5239 ©.
+contributor(s) : laurent modolo (2017)
+
+laurent.modolo@ens-lyon.fr
+
+This software is a computer program whose purpose is to manage dated file
+names in complience with the bioinformatic good practices used in the LBMC.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+--]=====]
+
+local root = "/Xnfs/lbmcdb/common/modules/apps/cdhit/4.6.8"
+
+conflict("cdhit")
+
+whatis([===[loads cdhit 4.6.8 (Debian 9) environment ]===])
+prepend_path{"PATH", pathJoin(root, "bin")}
+setenv("CDHIT_PATH", pathJoin(root, "bin"))
+
diff --git a/modulefiles/deeptools/3.0.2.lua b/modulefiles/deeptools/3.0.2.lua
index 3e078a6..70f6e75 100644
--- a/modulefiles/deeptools/3.0.2.lua
+++ b/modulefiles/deeptools/3.0.2.lua
@@ -34,8 +34,8 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
--]=====]
-local root = "/Xnfs/lbmcdb/common/modules/apps/deepTools/3.0.2"
-conflict("deepTools")
+local root = "/Xnfs/lbmcdb/common/modules/apps/deeptools/3.0.2"
+conflict("deeptools")
conflict("Python/2.7.13")
load("Python/3.6.1")
prereq_any("Python/3.6.1")
diff --git a/modulefiles/fastqc/0.11.5.lua b/modulefiles/fastqc/0.11.5.lua
index 46400f2..79765fd 100644
--- a/modulefiles/fastqc/0.11.5.lua
+++ b/modulefiles/fastqc/0.11.5.lua
@@ -34,10 +34,10 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
--]=====]
-local root = "/Xnfs/lbmcdb/common/modules/apps/FastQC/0.11.5"
+local root = "/Xnfs/lbmcdb/common/modules/apps/fastqc/0.11.5"
-conflict("FastQC")
+conflict("fastqc")
-whatis([===[loads FastQC 0.11.5 (Debian 9) environment ]===])
+whatis([===[loads fastqc 0.11.5 (Debian 9) environment ]===])
prepend_path{"PATH", pathJoin(root, "bin")}
setenv("FASTQC_PATH", pathJoin(root, "bin"))
diff --git a/modulefiles/gatk/4.0.10.1.lua b/modulefiles/gatk/4.0.10.1.lua
index b1b6ef3..7c4bf3d 100644
--- a/modulefiles/gatk/4.0.10.1.lua
+++ b/modulefiles/gatk/4.0.10.1.lua
@@ -34,12 +34,12 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
--]=====]
-local root = "/Xnfs/lbmcdb/common/modules/apps/GATK/4.0.10.1"
+local root = "/Xnfs/lbmcdb/common/modules/apps/gatk/4.0.10.1"
-conflict("GATK")
+conflict("gatk")
load("Java/1.8.0_151")
prereq_any("Java/1.8.0_151")
-whatis([===[loads GATK 4.0.10.1 (Debian 9) environment ]===])
+whatis([===[loads gatk 4.0.10.1 (Debian 9) environment ]===])
prepend_path{"PATH", pathJoin(root, "bin")}
-setenv("NEXTFLOW_PATH", pathJoin(root, "bin"))
+setenv("GATK_PATH", pathJoin(root, "bin"))
diff --git a/modulefiles/htseq/0.8.0.lua b/modulefiles/htseq/0.8.0.lua
index 6abf4c4..8dedfcc 100644
--- a/modulefiles/htseq/0.8.0.lua
+++ b/modulefiles/htseq/0.8.0.lua
@@ -34,8 +34,8 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
--]=====]
-local root = "/Xnfs/lbmcdb/common/modules/apps/HTSeq/0.8.0"
-conflict("HTSeq")
+local root = "/Xnfs/lbmcdb/common/modules/apps/htseq/0.8.0"
+conflict("htseq")
conflict("Python/3.6.1")
load("Python/2.7.13")
prereq_any("Python/2.7.13")
diff --git a/modulefiles/htseq/0.9.1.lua b/modulefiles/htseq/0.9.1.lua
index 40480ca..77d97b3 100644
--- a/modulefiles/htseq/0.9.1.lua
+++ b/modulefiles/htseq/0.9.1.lua
@@ -34,8 +34,8 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
--]=====]
-local root = "/Xnfs/lbmcdb/common/modules/apps/HTSeq/0.9.1"
-conflict("HTSeq")
+local root = "/Xnfs/lbmcdb/common/modules/apps/htseq/0.9.1"
+conflict("htseq")
conflict("Python/3.6.1")
load("Python/2.7.13")
prereq_any("Python/2.7.13")
diff --git a/modulefiles/rsem/1.3.0.lua b/modulefiles/rsem/1.3.0.lua
index 549d2f7..0bd5755 100644
--- a/modulefiles/rsem/1.3.0.lua
+++ b/modulefiles/rsem/1.3.0.lua
@@ -34,10 +34,10 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
--]=====]
-local root = "/Xnfs/lbmcdb/common/modules/apps/RSEM/1.3.0"
-setenv("LAST_MODULE","RSEM/1.3.0")
-whatis([===[loads RSEM 1.3.0 (Debian 9) environment ]===])
-conflict("RSEM")
+local root = "/Xnfs/lbmcdb/common/modules/apps/rsem/1.3.0"
+setenv("LAST_MODULE","rsem/1.3.0")
+whatis([===[loads rsem 1.3.0 (Debian 9) environment ]===])
+conflict("rsem")
conflict("Python/3.6.1")
load("Python/2.7.13")
load("Bowtie2/2.3.2")
diff --git a/modulefiles/rsem/1.3.1.lua b/modulefiles/rsem/1.3.1.lua
index cf39175..4fb9682 100644
--- a/modulefiles/rsem/1.3.1.lua
+++ b/modulefiles/rsem/1.3.1.lua
@@ -34,10 +34,10 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
--]=====]
-local root = "/Xnfs/lbmcdb/common/modules/apps/RSEM/1.3.1"
-setenv("LAST_MODULE","RSEM/1.3.1")
-whatis([===[loads RSEM 1.3.1 (Debian 9) environment ]===])
-conflict("RSEM")
+local root = "/Xnfs/lbmcdb/common/modules/apps/rsem/1.3.1"
+setenv("LAST_MODULE","rsem/1.3.1")
+whatis([===[loads rsem 1.3.1 (Debian 9) environment ]===])
+conflict("rsem")
conflict("Python/3.6.1")
load("Python/2.7.13")
load("Bowtie2/2.3.2")
diff --git a/modulefiles/salmon/0.8.2.lua b/modulefiles/salmon/0.8.2.lua
index 8d73c47..29bb5a6 100644
--- a/modulefiles/salmon/0.8.2.lua
+++ b/modulefiles/salmon/0.8.2.lua
@@ -34,10 +34,10 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
--]=====]
-local root = "/Xnfs/lbmcdb/common/modules/apps/Salmon/0.8.2"
-setenv("LAST_MODULE","Salmon/0.8.2")
-whatis([===[loads Salmon 0.8.2 (Debian 9) environment ]===])
-conflict("Salmon")
+local root = "/Xnfs/lbmcdb/common/modules/apps/salmon/0.8.2"
+setenv("LAST_MODULE","salmon/0.8.2")
+whatis([===[loads salmon 0.8.2 (Debian 9) environment ]===])
+conflict("salmon")
prepend_path{"PATH",pathJoin(root, "/bin"),delim=":",priority="0"}
prepend_path{"LD_LIBRARY_PATH",pathJoin(root, "/lib"),delim=":",priority="0"}
setenv("SALMON_PATH",pathJoin(root, "/bin"))
diff --git a/modulefiles/samtools/1.5.lua b/modulefiles/samtools/1.5.lua
index 54b3bc4..f525391 100644
--- a/modulefiles/samtools/1.5.lua
+++ b/modulefiles/samtools/1.5.lua
@@ -34,10 +34,10 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
--]=====]
-local root = "/Xnfs/lbmcdb/common/modules/apps/SAMtools/1.5/"
+local root = "/Xnfs/lbmcdb/common/modules/apps/samtools/1.5/"
-conflict("SAMtools")
+conflict("samtools")
-whatis([===[loads SAMtools 1.5 (Debian 9) environment ]===])
+whatis([===[loads samtools 1.5 (Debian 9) environment ]===])
prepend_path{"PATH", pathJoin(root, "bin")}
-setenv("SRATOOLKIT_PATH", pathJoin(root, "bin"))
+setenv("SAMTOOLS_PATH", pathJoin(root, "bin"))
diff --git a/modulefiles/samtools/1.7.lua b/modulefiles/samtools/1.7.lua
index d338538..5b77317 100644
--- a/modulefiles/samtools/1.7.lua
+++ b/modulefiles/samtools/1.7.lua
@@ -34,10 +34,10 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
--]=====]
-local root = "/Xnfs/lbmcdb/common/modules/apps/SAMtools/1.7/"
+local root = "/Xnfs/lbmcdb/common/modules/apps/samtools/1.7/"
-conflict("SAMtools")
+conflict("samtools")
-whatis([===[loads SAMtools 1.7 (Debian 9) environment ]===])
+whatis([===[loads samtools 1.7 (Debian 9) environment ]===])
prepend_path{"PATH", pathJoin(root, "bin")}
-setenv("SRATOOLKIT_PATH", pathJoin(root, "bin"))
+setenv("SAMTOOLS_PATH", pathJoin(root, "bin"))
diff --git a/modulefiles/sratoolkit/2.8.2.lua b/modulefiles/sratoolkit/2.8.2.lua
index 3524a79..85f3ee9 100644
--- a/modulefiles/sratoolkit/2.8.2.lua
+++ b/modulefiles/sratoolkit/2.8.2.lua
@@ -34,10 +34,10 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
--]=====]
-local root = "/Xnfs/lbmcdb/common/modules/apps/SRAtoolkit/2.8.2/"
+local root = "/Xnfs/lbmcdb/common/modules/apps/sratoolkit/2.8.2/"
-conflict("SRAtoolkit")
+conflict("sratoolkit")
-whatis([===[loads SRAtoolkit 2.8.2 (Debian 9) environment ]===])
+whatis([===[loads sratoolkit 2.8.2 (Debian 9) environment ]===])
prepend_path{"PATH", pathJoin(root, "bin")}
setenv("SRATOOLKIT_PATH", pathJoin(root, "bin"))
diff --git a/modulefiles/tophat/2.1.1.lua b/modulefiles/tophat/2.1.1.lua
index 9471aad..6a4baee 100644
--- a/modulefiles/tophat/2.1.1.lua
+++ b/modulefiles/tophat/2.1.1.lua
@@ -34,7 +34,7 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
--]=====]
-local root = "/Xnfs/lbmcdb/common/modules/apps/TopHat/2.1.1"
+local root = "/Xnfs/lbmcdb/common/modules/apps/tophat/2.1.1"
conflict("tophat")
load("Bowtie2/2.3.4.1")
diff --git a/modulefiles/trimmomatic/0.37.lua b/modulefiles/trimmomatic/0.37.lua
index 19c0ab7..ba3255e 100644
--- a/modulefiles/trimmomatic/0.37.lua
+++ b/modulefiles/trimmomatic/0.37.lua
@@ -34,10 +34,10 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
--]=====]
-local root = "/Xnfs/lbmcdb/common/modules/apps/Trimmomatic/0.36/bin"
-setenv("LAST_MODULE","Trimmomatic/0.36")
-whatis([===[loads Trimmomatic 0.36 (Debian 7) environment ]===])
-conflict("Trimmomatic")
+local root = "/Xnfs/lbmcdb/common/modules/apps/trimmomatic/0.36/bin"
+setenv("LAST_MODULE","trimmomatic/0.36")
+whatis([===[loads trimmomatic 0.36 (Debian 7) environment ]===])
+conflict("trimmomatic")
prepend_path{"PATH",pathJoin(root, "/bin"),delim=":",priority="0"}
setenv("TRIMMOMATIC_PATH",pathJoin(root, "/bin"))
diff --git a/modulefiles/urqt/d62c1f8.lua b/modulefiles/urqt/d62c1f8.lua
index dea0237..06e0a49 100644
--- a/modulefiles/urqt/d62c1f8.lua
+++ b/modulefiles/urqt/d62c1f8.lua
@@ -34,9 +34,9 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
--]=====]
-local root = "/Xnfs/lbmcdb/common/modules/apps/UrQt/d62c1f8"
-setenv("LAST_MODULE","UrQt/d62c1f8")
-whatis([===[loads UrQt d62c1f8 (Debian 7) environment ]===])
-conflict("UrQt")
+local root = "/Xnfs/lbmcdb/common/modules/apps/urqt/d62c1f8"
+setenv("LAST_MODULE","urqt/d62c1f8")
+whatis([===[loads urqt d62c1f8 (Debian 7) environment ]===])
+conflict("urqt")
prepend_path{"PATH",pathJoin(root, "/bin"),delim=":",priority="0"}
setenv("URQT_PATH",pathJoin(root, "/bin"))
--
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