diff --git a/apps/BCFtools/install_1.7.sh b/apps/bcftools/install_1.7.sh
similarity index 100%
rename from apps/BCFtools/install_1.7.sh
rename to apps/bcftools/install_1.7.sh
diff --git a/apps/BEDtools/install_2.25.0.sh b/apps/bedtools/install_2.25.0.sh
similarity index 100%
rename from apps/BEDtools/install_2.25.0.sh
rename to apps/bedtools/install_2.25.0.sh
diff --git a/apps/Bowtie2/install_2.3.2.sh b/apps/bowtie2/install_2.3.2.sh
similarity index 100%
rename from apps/Bowtie2/install_2.3.2.sh
rename to apps/bowtie2/install_2.3.2.sh
diff --git a/apps/Bowtie2/install_2.3.4.1.sh b/apps/bowtie2/install_2.3.4.1.sh
similarity index 100%
rename from apps/Bowtie2/install_2.3.4.1.sh
rename to apps/bowtie2/install_2.3.4.1.sh
diff --git a/apps/CDHIT/install_4.6.8.sh b/apps/cdhit/install_4.6.8.sh
similarity index 100%
rename from apps/CDHIT/install_4.6.8.sh
rename to apps/cdhit/install_4.6.8.sh
diff --git a/apps/deepTools/install_3.0.2.sh b/apps/deeptools/install_3.0.2.sh
similarity index 100%
rename from apps/deepTools/install_3.0.2.sh
rename to apps/deeptools/install_3.0.2.sh
diff --git a/apps/FastQC/install_0.11.5.sh b/apps/fastqc/install_0.11.5.sh
similarity index 100%
rename from apps/FastQC/install_0.11.5.sh
rename to apps/fastqc/install_0.11.5.sh
diff --git a/apps/GATK/install_4.0.10.1.sh b/apps/gatk/install_4.0.10.1.sh
similarity index 100%
rename from apps/GATK/install_4.0.10.1.sh
rename to apps/gatk/install_4.0.10.1.sh
diff --git a/apps/HTSeq/install_0.8.0.sh b/apps/htseq/install_0.8.0.sh
similarity index 100%
rename from apps/HTSeq/install_0.8.0.sh
rename to apps/htseq/install_0.8.0.sh
diff --git a/apps/HTSeq/install_0.9.1.sh b/apps/htseq/install_0.9.1.sh
similarity index 100%
rename from apps/HTSeq/install_0.9.1.sh
rename to apps/htseq/install_0.9.1.sh
diff --git a/apps/Kallisto/install_0.43.1.sh b/apps/kallisto/install_0.43.1.sh
similarity index 100%
rename from apps/Kallisto/install_0.43.1.sh
rename to apps/kallisto/install_0.43.1.sh
diff --git a/apps/Kallisto/install_0.44.0.sh b/apps/kallisto/install_0.44.0.sh
similarity index 100%
rename from apps/Kallisto/install_0.44.0.sh
rename to apps/kallisto/install_0.44.0.sh
diff --git a/apps/MACS2/install_2.1.1.20160309.sh b/apps/macs2/install_2.1.2.sh
similarity index 98%
rename from apps/MACS2/install_2.1.1.20160309.sh
rename to apps/macs2/install_2.1.2.sh
index 1ea33819b77de80778abc6766e8e4de12ea02480..5ea00c05cf90388cef5be7059b5f5738d39e0ba4 100644
--- a/apps/MACS2/install_2.1.1.20160309.sh
+++ b/apps/macs2/install_2.1.2.sh
@@ -36,7 +36,7 @@
 source ../build_env.sh
 module load Python/2.7.13
 
-MACS2_VERSION=2.1.1.20160309
+MACS2_VERSION=2.1.2
 MACS2_ROOT=/Xnfs/lbmcdb/common/modules/apps/MACS2/${MACS2_VERSION}
 mkdir -p ${MACS2_VERSION}/lib/python2.7/dist-packages/
 PYTHONPATH=${MACS2_ROOT}lib/python2.7/dist-packages/:$PYTHONPATH
diff --git a/apps/MultiQC/install_0.9.sh b/apps/multiqc/install_0.9.sh
similarity index 100%
rename from apps/MultiQC/install_0.9.sh
rename to apps/multiqc/install_0.9.sh
diff --git a/apps/MultiQC/install_1.0.sh b/apps/multiqc/install_1.0.sh
similarity index 100%
rename from apps/MultiQC/install_1.0.sh
rename to apps/multiqc/install_1.0.sh
diff --git a/apps/MUSIC/install_6613c53.sh b/apps/music/install_6613c53.sh
similarity index 100%
rename from apps/MUSIC/install_6613c53.sh
rename to apps/music/install_6613c53.sh
diff --git a/apps/RSEM/install_1.3.0.sh b/apps/rsem/install_1.3.0.sh
similarity index 100%
rename from apps/RSEM/install_1.3.0.sh
rename to apps/rsem/install_1.3.0.sh
diff --git a/apps/RSEM/install_1.3.1.sh b/apps/rsem/install_1.3.1.sh
similarity index 100%
rename from apps/RSEM/install_1.3.1.sh
rename to apps/rsem/install_1.3.1.sh
diff --git a/apps/Salmon/install_0.8.2.sh b/apps/salmon/install_0.8.2.sh
similarity index 100%
rename from apps/Salmon/install_0.8.2.sh
rename to apps/salmon/install_0.8.2.sh
diff --git a/apps/SAMtools/install_1.5.sh b/apps/samtools/install_1.5.sh
similarity index 100%
rename from apps/SAMtools/install_1.5.sh
rename to apps/samtools/install_1.5.sh
diff --git a/apps/SAMtools/install_1.7.sh b/apps/samtools/install_1.7.sh
similarity index 100%
rename from apps/SAMtools/install_1.7.sh
rename to apps/samtools/install_1.7.sh
diff --git a/apps/SRAtoolkit/install_2.8.2.sh b/apps/sratoolkit/install_2.8.2.sh
similarity index 100%
rename from apps/SRAtoolkit/install_2.8.2.sh
rename to apps/sratoolkit/install_2.8.2.sh
diff --git a/apps/TopHat/install_2.1.1.sh b/apps/tophat/install_2.1.1.sh
similarity index 100%
rename from apps/TopHat/install_2.1.1.sh
rename to apps/tophat/install_2.1.1.sh
diff --git a/apps/Trimmomatic/install_0.36.sh b/apps/trimmomatic/install_0.36.sh
similarity index 100%
rename from apps/Trimmomatic/install_0.36.sh
rename to apps/trimmomatic/install_0.36.sh
diff --git a/apps/UrQt/install_d62c1f8.sh b/apps/urqt/install_d62c1f8.sh
similarity index 100%
rename from apps/UrQt/install_d62c1f8.sh
rename to apps/urqt/install_d62c1f8.sh
diff --git a/modulefiles/CDHIT/4.6.8 b/modulefiles/CDHIT/4.6.8
deleted file mode 100644
index 8a48a7f1ea480fd6069b987b31c290727f23c282..0000000000000000000000000000000000000000
--- 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/SAMtools/1.7.lua b/modulefiles/bcftools/1.7.lua
similarity index 90%
rename from modulefiles/SAMtools/1.7.lua
rename to modulefiles/bcftools/1.7.lua
index d33853842503243edfd70a83041e2f287c465e9f..66886f2b26c44da1bb1b059d68e2bf1220bc91a5 100644
--- a/modulefiles/SAMtools/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/SAMtools/1.7/"
+local root = "/Xnfs/lbmcdb/common/modules/apps/bcftools/1.7/"
 
-conflict("SAMtools")
+conflict("bcftools")
 
-whatis([===[loads SAMtools 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
similarity index 92%
rename from modulefiles/BEDtools/2.25.0.lua
rename to modulefiles/bedtools/2.25.0.lua
index 3bb7e4e2f1f64ed636959cb792d6c068a1755fa1..72e6f88d56a065d3c9242b200a6d55414f82e6ed 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
similarity index 92%
rename from modulefiles/Bowtie2/2.3.2.lua
rename to modulefiles/bowtie2/2.3.2.lua
index 59c73b542c5979704ab7804eed3c24b3e89f4048..b165552b4196f0321f1a185ccef3ee7f0008731e 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
similarity index 92%
rename from modulefiles/Bowtie2/2.3.4.1.lua
rename to modulefiles/bowtie2/2.3.4.1.lua
index cfdd1d158e6c76309fd155236799a8fa3b316498..50104b408e11a171d9d37b55f45876f12c855871 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.lua b/modulefiles/cdhit/4.6.8.lua
new file mode 100644
index 0000000000000000000000000000000000000000..762e845a7c00d15b260b472f7923e702627fc970
--- /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
similarity index 95%
rename from modulefiles/deepTools/3.0.2.lua
rename to modulefiles/deeptools/3.0.2.lua
index 3e078a68386f9961ff6e51a0f0c47c6d49d5340f..70f6e7544b12658a28d8c19274fb11885d590574 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
similarity index 92%
rename from modulefiles/FastQC/0.11.5.lua
rename to modulefiles/fastqc/0.11.5.lua
index 46400f22ddc4ced359b2a654914b2f9cc5b5a7ba..79765fdf462bab98c48f41e4986512c261a24bc7 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
similarity index 90%
rename from modulefiles/GATK/4.0.10.1.lua
rename to modulefiles/gatk/4.0.10.1.lua
index b1b6ef3fa8c5fc1650bdf335ffefd663885b5527..7c4bf3d9f43bdea0006bca089e933cc7baa629d7 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
similarity index 96%
rename from modulefiles/HTSeq/0.8.0.lua
rename to modulefiles/htseq/0.8.0.lua
index 6abf4c437294dd47f52a5ee2be5746063140cdd7..8dedfccb99fe57f4487b965b170f377c951ecfe3 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
similarity index 96%
rename from modulefiles/HTSeq/0.9.1.lua
rename to modulefiles/htseq/0.9.1.lua
index 40480ca5404c5d52859d748aea74f2f7b38175f6..77d97b32eb24a714af7eaae42b18a7db142af12a 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/Kallisto/0.43.1.lua b/modulefiles/kallisto/0.43.1.lua
similarity index 100%
rename from modulefiles/Kallisto/0.43.1.lua
rename to modulefiles/kallisto/0.43.1.lua
diff --git a/modulefiles/Kallisto/0.44.0.lua b/modulefiles/kallisto/0.44.0.lua
similarity index 100%
rename from modulefiles/Kallisto/0.44.0.lua
rename to modulefiles/kallisto/0.44.0.lua
diff --git a/modulefiles/MACS2/2.1.1.20160309.lua b/modulefiles/macs2/2.1.2.lua
similarity index 97%
rename from modulefiles/MACS2/2.1.1.20160309.lua
rename to modulefiles/macs2/2.1.2.lua
index 86856a5734aff83cbd58354d8bc512d6dec558fd..6a5db78ef02f11e0847cea61977752a4868ac1e4 100644
--- a/modulefiles/MACS2/2.1.1.20160309.lua
+++ b/modulefiles/macs2/2.1.2.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/MACS2/1.0"
+local root = "/Xnfs/lbmcdb/common/modules/apps/macs2/2.1.2"
 conflict("MACS2")
 conflict("Python/3.6.1")
 load("Python/2.7.13")
diff --git a/modulefiles/MultiQC/0.9 b/modulefiles/multiqc/0.9
similarity index 100%
rename from modulefiles/MultiQC/0.9
rename to modulefiles/multiqc/0.9
diff --git a/modulefiles/MultiQC/1.0.lua b/modulefiles/multiqc/1.0.lua
similarity index 100%
rename from modulefiles/MultiQC/1.0.lua
rename to modulefiles/multiqc/1.0.lua
diff --git a/modulefiles/MUSIC/6613c53.lua b/modulefiles/music/6613c53.lua
similarity index 100%
rename from modulefiles/MUSIC/6613c53.lua
rename to modulefiles/music/6613c53.lua
diff --git a/modulefiles/RSEM/1.3.0.lua b/modulefiles/rsem/1.3.0.lua
similarity index 92%
rename from modulefiles/RSEM/1.3.0.lua
rename to modulefiles/rsem/1.3.0.lua
index 549d2f752f3a38227738fa09cabd3d590f1c7987..0bd575542ee6ace27cd4df0b7fcd270fc911a9f5 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
similarity index 92%
rename from modulefiles/RSEM/1.3.1.lua
rename to modulefiles/rsem/1.3.1.lua
index cf39175b5741f65558fe31d2f880a1238394fe47..4fb96821828b2cc683aaf4591aa4d9703d35a20d 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
similarity index 91%
rename from modulefiles/Salmon/0.8.2.lua
rename to modulefiles/salmon/0.8.2.lua
index 8d73c478496bb55374367218c55bb8013ae58ab9..29bb5a61c3a66123c5b4abfea7907a58b90908a6 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
similarity index 90%
rename from modulefiles/SAMtools/1.5.lua
rename to modulefiles/samtools/1.5.lua
index 54b3bc4ec932c1fb3ca024584312daa200eddc68..f525391eaa6a2c7e05a7ea5ab90265cb530483a9 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/BCFtools/1.7.lua b/modulefiles/samtools/1.7.lua
similarity index 90%
rename from modulefiles/BCFtools/1.7.lua
rename to modulefiles/samtools/1.7.lua
index a25b615c5d426d851323108c6afa4e2ee9aef214..5b7731777a9363a6bf0f2655fd779959fd9d0477 100644
--- a/modulefiles/BCFtools/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/BCFtools/1.7/"
+local root = "/Xnfs/lbmcdb/common/modules/apps/samtools/1.7/"
 
-conflict("BCFtools")
+conflict("samtools")
 
-whatis([===[loads BCFtools 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
similarity index 92%
rename from modulefiles/SRAtoolkit/2.8.2.lua
rename to modulefiles/sratoolkit/2.8.2.lua
index 3524a79aeb5796c57a3d5e29543af1e339bba408..85f3ee94041b08d413c0bdf1cebf08c796361806 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
similarity index 96%
rename from modulefiles/TopHat/2.1.1.lua
rename to modulefiles/tophat/2.1.1.lua
index 9471aadc5ba11f5dcf2c95bfc7414a04fdd8444c..6a4baee5a4a07645cbdb4d2786083b0b530b3211 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
similarity index 90%
rename from modulefiles/Trimmomatic/0.37.lua
rename to modulefiles/trimmomatic/0.37.lua
index 19c0ab7c63d18fd2fc82feb33143d3412ec72c46..ba3255e84f6bd7c3e88b940b6a018154990d4780 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
similarity index 91%
rename from modulefiles/UrQt/d62c1f8.lua
rename to modulefiles/urqt/d62c1f8.lua
index dea02372033bddddee271629c146311b8acaca23..06e0a49e7f942895a90df7513ca48f536a0da00c 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"))