Merge branch 'master' of gitlab_lbmc:PSMN/modules

modulefiles/CDHIT/4.6.8

-#%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

modulefiles/SAMtools/1.7.lua → 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"))

modulefiles/BEDtools/2.25.0.lua → 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"))

modulefiles/Bowtie2/2.3.2.lua → 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"))

modulefiles/Bowtie2/2.3.4.1.lua → 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"))

modulefiles/cdhit/4.6.8.lua

+--[=====[
+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"))
+

modulefiles/deepTools/3.0.2.lua → 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")

modulefiles/FastQC/0.11.5.lua → 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"))

modulefiles/GATK/4.0.10.1.lua → 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"))

modulefiles/HTSeq/0.8.0.lua → 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")

modulefiles/HTSeq/0.9.1.lua → 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")

modulefiles/MACS2/2.1.1.20160309.lua → 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")