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"))