Merge branch 'master' of gitlab_lbmc:PSMN/modules

modulefiles/RSEM/1.3.0.lua → 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")

modulefiles/RSEM/1.3.1.lua → 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")

modulefiles/Salmon/0.8.2.lua → 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"))

modulefiles/SAMtools/1.5.lua → 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"))

modulefiles/BCFtools/1.7.lua → 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"))

modulefiles/SRAtoolkit/2.8.2.lua → 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"))

modulefiles/TopHat/2.1.1.lua → 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")

modulefiles/Trimmomatic/0.37.lua → 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"))
 

modulefiles/UrQt/d62c1f8.lua → 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"))