From 2ccdb5447df11f80a70f9b609ff4b9a03b1b8bf6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Dernat=20R=C3=A9my?= <remy.dernat@umontpellier.fr>
Date: Fri, 21 Feb 2020 14:58:43 +0100
Subject: [PATCH] reorganize + go /home/dernatremy to set GOPATH
---
envfiles/R-3.0.3 | 24 --------
envfiles/R-3.1.3 | 24 --------
envfiles/R-3.2.0 | 24 --------
envfiles/R-3.3.1 | 56 -------------------
envfiles/R-3.4.3 | 51 -----------------
envfiles/R-3.5.3 | 49 ----------------
envfiles/R-343-jags | 51 -----------------
envfiles/abyss-2.0.2 | 2 +-
envfiles/bamm2.5.0 | 2 +-
envfiles/bcftools-1.3 | 4 +-
envfiles/beagle-libs-2.1.2 | 2 +-
envfiles/blast-2.6.0 | 50 -----------------
envfiles/blast-2.8.1 | 50 -----------------
envfiles/cmake-3.10.0 | 2 +-
envfiles/dapl1.2 | 22 --------
envfiles/dapl2 | 24 --------
envfiles/deprecated/openmpi-1.6.2 | 2 +-
.../deprecated/singularity/singularity-2.4.2 | 2 +-
envfiles/gcc-current-7 | 54 ------------------
envfiles/gcc4.9 | 24 --------
envfiles/gcc5.3 | 53 ------------------
envfiles/gcc5.4 | 48 ----------------
envfiles/gdal-2.1.2 | 2 +-
envfiles/golang-1.11 | 25 ---------
envfiles/golang-1.13.1 | 31 ----------
envfiles/hdf5-1.8.18 | 26 ---------
envfiles/hdf5-1.8.9-el6 | 26 ---------
envfiles/hdf5parallel-1.8.18 | 53 ------------------
envfiles/libgeos-3.3.8 | 22 --------
envfiles/libgeos_c-1.7.8 | 22 --------
envfiles/libz-1.2.11 | 23 --------
envfiles/libz-1.2.6 | 23 --------
envfiles/libz-1.2.8 | 46 ---------------
envfiles/netcdf-4.3.3.1 | 22 --------
envfiles/netcdf-4.4.1.1 | 23 --------
envfiles/openmpi-4.0.1 | 2 +-
envfiles/openssl-1.1.0b | 24 --------
envfiles/openssl-3.0.0 | 24 --------
envfiles/openssl-devel-1.0.1e | 33 -----------
envfiles/samtools0.1.19 | 24 --------
envfiles/samtools1.3 | 54 ------------------
envfiles/singularity-2.4.1 | 23 --------
envfiles/singularity-2.6 | 23 --------
envfiles/singularity-3.1 | 25 ---------
envfiles/singularity-3.4.2 | 25 ---------
envfiles/stacks1.37 | 25 ---------
envfiles/stacks1.40 | 25 ---------
envfiles/stacks1.46 | 51 -----------------
envfiles/stacks1.48 | 51 -----------------
envfiles/stacks2.0beta | 51 -----------------
envfiles/stacks2.0beta.10a | 52 -----------------
envfiles/tabix-0.2.6 | 2 +-
envfiles/vcftools-0.1.15 | 4 +-
53 files changed, 13 insertions(+), 1469 deletions(-)
delete mode 100644 envfiles/R-3.0.3
delete mode 100644 envfiles/R-3.1.3
delete mode 100644 envfiles/R-3.2.0
delete mode 100644 envfiles/R-3.3.1
delete mode 100644 envfiles/R-3.4.3
delete mode 100644 envfiles/R-3.5.3
delete mode 100644 envfiles/R-343-jags
delete mode 100644 envfiles/blast-2.6.0
delete mode 100644 envfiles/blast-2.8.1
delete mode 100644 envfiles/dapl1.2
delete mode 100644 envfiles/dapl2
delete mode 100644 envfiles/gcc-current-7
delete mode 100644 envfiles/gcc4.9
delete mode 100644 envfiles/gcc5.3
delete mode 100644 envfiles/gcc5.4
delete mode 100644 envfiles/golang-1.11
delete mode 100644 envfiles/golang-1.13.1
delete mode 100644 envfiles/hdf5-1.8.18
delete mode 100644 envfiles/hdf5-1.8.9-el6
delete mode 100644 envfiles/hdf5parallel-1.8.18
delete mode 100644 envfiles/libgeos-3.3.8
delete mode 100644 envfiles/libgeos_c-1.7.8
delete mode 100644 envfiles/libz-1.2.11
delete mode 100644 envfiles/libz-1.2.6
delete mode 100644 envfiles/libz-1.2.8
delete mode 100644 envfiles/netcdf-4.3.3.1
delete mode 100644 envfiles/netcdf-4.4.1.1
delete mode 100644 envfiles/openssl-1.1.0b
delete mode 100644 envfiles/openssl-3.0.0
delete mode 100644 envfiles/openssl-devel-1.0.1e
delete mode 100644 envfiles/samtools0.1.19
delete mode 100644 envfiles/samtools1.3
delete mode 100644 envfiles/singularity-2.4.1
delete mode 100644 envfiles/singularity-2.6
delete mode 100644 envfiles/singularity-3.1
delete mode 100644 envfiles/singularity-3.4.2
delete mode 100644 envfiles/stacks1.37
delete mode 100644 envfiles/stacks1.40
delete mode 100644 envfiles/stacks1.46
delete mode 100644 envfiles/stacks1.48
delete mode 100644 envfiles/stacks2.0beta
delete mode 100644 envfiles/stacks2.0beta.10a
diff --git a/envfiles/R-3.0.3 b/envfiles/R-3.0.3
deleted file mode 100644
index 5e2a98c..0000000
--- a/envfiles/R-3.0.3
+++ /dev/null
@@ -1,24 +0,0 @@
-#%Module######################################################################
-#
-# R-3.0.3 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use R-3.0.3"
-puts stderr "The program R-3.0.3"
-puts stderr "is added to PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set R_LEVEL 3.0.3
-set R_CURPATH /share/apps/bin/R/R-$R_LEVEL
-
-prepend-path PATH $R_CURPATH/bin/
-prepend-path LD_LIBRARY_PATH $R_CURPATH/lib64/R/lib
-prepend-path MANPATH $R_CURPATH/share/man
-
-append-path PE_PRODUCT_LIST R-$R_LEVEL
-setenv R_LIBS $R_CURPATH/lib64/R/library
diff --git a/envfiles/R-3.1.3 b/envfiles/R-3.1.3
deleted file mode 100644
index 817d3e3..0000000
--- a/envfiles/R-3.1.3
+++ /dev/null
@@ -1,24 +0,0 @@
-#%Module######################################################################
-#
-# R-3.1.3 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use R-3.1.3"
-puts stderr "The program R-3.1.3"
-puts stderr "is added to PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set R_LEVEL 3.1.3
-set R_CURPATH /share/apps/bin/R/R-$R_LEVEL
-
-prepend-path PATH $R_CURPATH/bin/
-prepend-path LD_LIBRARY_PATH $R_CURPATH/lib64/R/lib
-prepend-path MANPATH $R_CURPATH/share/man
-
-append-path PE_PRODUCT_LIST R-$R_LEVEL
-setenv R_LIBS $R_CURPATH/lib64/R/library
diff --git a/envfiles/R-3.2.0 b/envfiles/R-3.2.0
deleted file mode 100644
index 30ef455..0000000
--- a/envfiles/R-3.2.0
+++ /dev/null
@@ -1,24 +0,0 @@
-#%Module######################################################################
-#
-# R-3.2.0 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use R-3.2.0"
-puts stderr "The program R-3.2.0"
-puts stderr "is added to PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set R_LEVEL 3.2.0
-set R_CURPATH /share/apps/bin/R/R-$R_LEVEL
-
-prepend-path PATH $R_CURPATH/bin/
-prepend-path LD_LIBRARY_PATH $R_CURPATH/lib64/R/lib
-prepend-path MANPATH $R_CURPATH/share/man
-
-append-path PE_PRODUCT_LIST R-$R_LEVEL
-setenv R_LIBS $R_CURPATH/lib64/R/library
diff --git a/envfiles/R-3.3.1 b/envfiles/R-3.3.1
deleted file mode 100644
index 08091f5..0000000
--- a/envfiles/R-3.3.1
+++ /dev/null
@@ -1,56 +0,0 @@
-#%Module######################################################################
-#
-# R-3.3.1 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use R-3.3.1"
-puts stderr "The program R-3.3.1"
-puts stderr "is added to PATH."
-}
-
-set rel [uname release]
-global prodlist
-set prodlist {xz-5.2.2 openssl-1.1.0b \
- atlas curl-7.50.3 \
- pcre-8.39 }
-
-
-set is_module_rm [module-info mode remove]
-
-catch {set modulehomes $env(MODULEPATH)}
-if { [ module-info mode load ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module load $prod
- }
- }
- }
-}
-
-if { [ module-info mode remove ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module unload $prod
- }
- }
- }
-}
-
-
-set R_LEVEL 3.3.1
-set R_CURPATH /share/apps/bin/R/R-$R_LEVEL
-
-prepend-path PATH $R_CURPATH/bin/
-if { $rel == "2.6.32-504.16.2.el6.x86_64" } {
- prepend-path LD_LIBRARY_PATH $R_CURPATH/lib64/R/lib
-} else {
- prepend-path LD_LIBRARY_PATH /share/apps/lib/atlas/3.0:$R_CURPATH/lib64/R/lib
-}
-prepend-path MANPATH $R_CURPATH/share/man
-
-append-path PE_PRODUCT_LIST R-$R_LEVEL
-setenv R_LIBS $R_CURPATH/lib64/R/library
diff --git a/envfiles/R-3.4.3 b/envfiles/R-3.4.3
deleted file mode 100644
index 016d711..0000000
--- a/envfiles/R-3.4.3
+++ /dev/null
@@ -1,51 +0,0 @@
-#%Module######################################################################
-#
-# R-3.4.3 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use R-3.4.3"
-puts stderr "The program $R-3.4.3"
-puts stderr "is added to PATH."
-}
-
-set rel [uname release]
-global prodlist
-set prodlist { singularity-2.4.1 }
-
-
-set is_module_rm [module-info mode remove]
-
-catch {set modulehomes $env(MODULEPATH)}
-if { [ module-info mode load ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module load $prod
- }
- }
- }
-}
-
-if { [ module-info mode remove ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module unload $prod
- unset-alias R
- unset-alias Rscript
- }
- }
- }
-}
-
-
-set R_LEVEL 3.4.3
-set-alias R "singularity run /share/apps/sing-images/2.4/R-3.4.3_from_source"
-set-alias Rscript "singularity exec /share/apps/sing-images/2.4/R-3.4.3_from_source Rscript"
-
-# aliases not passing through SGE. Would need to source a file...
-prepend-path PATH /share/apps/sing-images/2.4
-
-append-path PE_PRODUCT_LIST R-$R_LEVEL
diff --git a/envfiles/R-3.5.3 b/envfiles/R-3.5.3
deleted file mode 100644
index a38de6f..0000000
--- a/envfiles/R-3.5.3
+++ /dev/null
@@ -1,49 +0,0 @@
-#%Module######################################################################
-#
-# R-3.5.3 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use R-3.5.3"
-puts stderr "The program R-3.5.3"
-puts stderr "is added to PATH."
-}
-
-set rel [uname release]
-global prodlist
-set prodlist { singularity-3.1 }
-
-
-set is_module_rm [module-info mode remove]
-
-catch {set modulehomes $env(MODULEPATH)}
-if { [ module-info mode load ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module load $prod
- }
- }
- }
-}
-
-if { [ module-info mode remove ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module unload $prod
- unset-alias R
- unset-alias Rscript
- }
- }
- }
-}
-
-
-set R_LEVEL 3.5.3
-
-# aliases not passing through SGE. Would need to source a file...
-prepend-path PATH /share/apps/sing-images/3.1
-
-append-path PE_PRODUCT_LIST R-$R_LEVEL
diff --git a/envfiles/R-343-jags b/envfiles/R-343-jags
deleted file mode 100644
index 7168e30..0000000
--- a/envfiles/R-343-jags
+++ /dev/null
@@ -1,51 +0,0 @@
-#%Module######################################################################
-#
-# R-3.4.3 modulefile with rjags
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use R-3.4.3"
-puts stderr "The program $R-3.4.3"
-puts stderr "is added to PATH."
-}
-
-set rel [uname release]
-global prodlist
-set prodlist { singularity-2.4.1 }
-
-
-set is_module_rm [module-info mode remove]
-
-catch {set modulehomes $env(MODULEPATH)}
-if { [ module-info mode load ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module load $prod
- }
- }
- }
-}
-
-if { [ module-info mode remove ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module unload $prod
- unset-alias R
- unset-alias Rscript
- }
- }
- }
-}
-
-
-set R_LEVEL 3.4.3
-set-alias R "singularity run /share/apps/sing-images/2.4/R-343-jags"
-set-alias Rscript "singularity exec /share/apps/sing-images/2.4/R-343-jags"
-
-# aliases not passing through SGE. Would need to source a file...
-prepend-path PATH /share/apps/sing-images/2.4
-
-append-path PE_PRODUCT_LIST R-$R_LEVEL
diff --git a/envfiles/abyss-2.0.2 b/envfiles/abyss-2.0.2
index f8d7799..d81bac7 100644
--- a/envfiles/abyss-2.0.2
+++ b/envfiles/abyss-2.0.2
@@ -14,7 +14,7 @@ set rel [uname release]
global prodlist
# libz does not seem to be mandatory
-set prodlist {gcc4.9 }
+set prodlist {gcc/4.9 }
set is_module_rm [module-info mode remove]
diff --git a/envfiles/bamm2.5.0 b/envfiles/bamm2.5.0
index 7ee1cce..a322ecb 100644
--- a/envfiles/bamm2.5.0
+++ b/envfiles/bamm2.5.0
@@ -10,7 +10,7 @@ puts stderr "is added to PATH."
}
global prodlist
-set prodlist {gcc4.9 }
+set prodlist {gcc/4.9 }
set is_module_rm [module-info mode remove]
diff --git a/envfiles/bcftools-1.3 b/envfiles/bcftools-1.3
index f0547c1..d34051b 100644
--- a/envfiles/bcftools-1.3
+++ b/envfiles/bcftools-1.3
@@ -14,9 +14,9 @@ set rel [uname release]
global prodlist
if { $rel == "2.6.32-504.16.2.el6.x86_64" } {
- set prodlist {libz-1.2.8 libc-2.14}
+ set prodlist {libz/1.2.8 libc/2.14}
} else {
- set prodlist {libz-1.2.8}
+ set prodlist {libz/1.2.8}
}
set is_module_rm [module-info mode remove]
diff --git a/envfiles/beagle-libs-2.1.2 b/envfiles/beagle-libs-2.1.2
index fdaec5d..2bb25b7 100644
--- a/envfiles/beagle-libs-2.1.2
+++ b/envfiles/beagle-libs-2.1.2
@@ -10,7 +10,7 @@ puts stderr "The library beagle"
puts stderr "is added to your LD_LIBRARY_PATH."
}
-set prodlist { gcc4.9 }
+set prodlist { gcc/4.9 }
set is_module_rm [module-info mode remove]
diff --git a/envfiles/blast-2.6.0 b/envfiles/blast-2.6.0
deleted file mode 100644
index d14272b..0000000
--- a/envfiles/blast-2.6.0
+++ /dev/null
@@ -1,50 +0,0 @@
-#%Module######################################################################
-#
-# Blast 2.6.0 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use Blast-2.6.0"
-puts stderr "The program Blast2.6.0"
-puts stderr "is added to PATH."
-}
-
-#set rel [uname release]
-global prodlist
-#set prodlist {gcc4.9 openssl-1.1.0b \
-# atlas openmpi-x86_64 }
-
-
-set is_module_rm [module-info mode remove]
-
-#catch {set modulehomes $env(MODULEPATH)}
-#if { [ module-info mode load ] } {
-# foreach prod $prodlist {
-# foreach mfilehome [ split $modulehomes :] {
-# if { [file exists $mfilehome/$prod] } {
-# module load $prod
-# }
-# }
-# }
-#}
-
-#if { [ module-info mode remove ] } {
-# foreach prod $prodlist {
-# foreach mfilehome [ split $modulehomes :] {
-# if { [file exists $mfilehome/$prod] } {
-# module unload $prod
-# }
-# }
-# }
-#}
-
-
-set BLAST_LEVEL 2.6.0
-set BLAST_CURPATH /share/apps/bin/blast/2/$BLAST_LEVEL
-
-prepend-path PATH $BLAST_CURPATH/bin/
-prepend-path LD_LIBRARY_PATH $BLAST_CURPATH/lib
-#prepend-path MANPATH $BLAST_CURPATH/share/man
-
-append-path PE_PRODUCT_LIST BLAST.$BLAST_LEVEL
diff --git a/envfiles/blast-2.8.1 b/envfiles/blast-2.8.1
deleted file mode 100644
index 7b95420..0000000
--- a/envfiles/blast-2.8.1
+++ /dev/null
@@ -1,50 +0,0 @@
-#%Module######################################################################
-#
-# Blast 2.6.0 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use Blast-2.8.1"
-puts stderr "The program Blast2.8.1"
-puts stderr "is added to PATH."
-}
-
-#set rel [uname release]
-global prodlist
-#set prodlist {gcc4.9 openssl-1.1.0b \
-# atlas openmpi-x86_64 }
-
-
-set is_module_rm [module-info mode remove]
-
-#catch {set modulehomes $env(MODULEPATH)}
-#if { [ module-info mode load ] } {
-# foreach prod $prodlist {
-# foreach mfilehome [ split $modulehomes :] {
-# if { [file exists $mfilehome/$prod] } {
-# module load $prod
-# }
-# }
-# }
-#}
-
-#if { [ module-info mode remove ] } {
-# foreach prod $prodlist {
-# foreach mfilehome [ split $modulehomes :] {
-# if { [file exists $mfilehome/$prod] } {
-# module unload $prod
-# }
-# }
-# }
-#}
-
-
-set BLAST_LEVEL 2.8.1
-set BLAST_CURPATH /share/apps/bin/blast/2/$BLAST_LEVEL
-
-prepend-path PATH $BLAST_CURPATH/bin/
-prepend-path LD_LIBRARY_PATH $BLAST_CURPATH/lib
-#prepend-path MANPATH $BLAST_CURPATH/share/man
-
-append-path PE_PRODUCT_LIST BLAST-$BLAST_LEVEL
diff --git a/envfiles/cmake-3.10.0 b/envfiles/cmake-3.10.0
index 33a8def..e2189ee 100644
--- a/envfiles/cmake-3.10.0
+++ b/envfiles/cmake-3.10.0
@@ -11,7 +11,7 @@ puts stderr "is added to PATH."
}
global prodlist
-set prodlist {gcc4.9}
+set prodlist {gcc/4.9}
set is_module_rm [module-info mode remove]
diff --git a/envfiles/dapl1.2 b/envfiles/dapl1.2
deleted file mode 100644
index e4ff0b0..0000000
--- a/envfiles/dapl1.2
+++ /dev/null
@@ -1,22 +0,0 @@
-#%Module######################################################################
-#
-# libdapl1.2 modulefile 20181127
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use the library lib dapl 1.2"
-puts stderr "The library dapl1.2 - The DAT API library https://www.openfabrics.org/"
-puts stderr "is added to your LD_LIBRARY_PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set LIBDAPL_LVL 1
-set LIBDAPL_SUBVER 2.19
-set LIBDAPL_CURPATH /share/apps/lib/dapl/$LIBDAPL_LVL.$LIBDAPL_SUBVER
-
-prepend-path LD_LIBRARY_PATH $LIBDAPL_CURPATH/lib
-
-append-path PE_PRODUCT_LIST LIBDAPL.$LIBDAPL_LVL.$LIBDAPL_SUBVER
diff --git a/envfiles/dapl2 b/envfiles/dapl2
deleted file mode 100644
index 741c3a1..0000000
--- a/envfiles/dapl2
+++ /dev/null
@@ -1,24 +0,0 @@
-#%Module######################################################################
-#
-# libdapl 2.0.34 modulefile 20181127
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use the library lib dapl 1.2"
-puts stderr "The library dapl1.2 - The DAT API library https://www.openfabrics.org/"
-puts stderr "is added to your LD_LIBRARY_PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set LIBDAPL_LVL 2
-set LIBDAPL_SUBVER 0.34
-set LIBDAPL_CURPATH /share/apps/lib/dapl/$LIBDAPL_LVL.$LIBDAPL_SUBVER.el6
-setenv C_INCLUDE_PATH $LIBDAPL_CURPATH/include
-setenv CPLUS_INCLUDE_PATH $LIBDAPL_CURPATH/include
-
-prepend-path LD_LIBRARY_PATH $LIBDAPL_CURPATH/lib
-
-append-path PE_PRODUCT_LIST LIBDAPL.$LIBDAPL_LVL.$LIBDAPL_SUBVER
diff --git a/envfiles/deprecated/openmpi-1.6.2 b/envfiles/deprecated/openmpi-1.6.2
index 0b4f015..b32fc81 100644
--- a/envfiles/deprecated/openmpi-1.6.2
+++ b/envfiles/deprecated/openmpi-1.6.2
@@ -32,7 +32,7 @@ global prodlist
conflict mpi
if { $rel != "2.6.32-504.16.2.el6.x86_64" } {
- set prodlist {dapl1.2}
+ set prodlist {dapl/1.2}
} else {
set prodlist {}
}
diff --git a/envfiles/deprecated/singularity/singularity-2.4.2 b/envfiles/deprecated/singularity/singularity-2.4.2
index 7605a41..d94ede9 100644
--- a/envfiles/deprecated/singularity/singularity-2.4.2
+++ b/envfiles/deprecated/singularity/singularity-2.4.2
@@ -12,7 +12,7 @@ puts stderr "is added to PATH."
set rel [uname release]
global prodlist
-set prodlist { gcc5.3 }
+set prodlist { gcc/5.3 }
set is_module_rm [module-info mode remove]
diff --git a/envfiles/gcc-current-7 b/envfiles/gcc-current-7
deleted file mode 100644
index 8a9698a..0000000
--- a/envfiles/gcc-current-7
+++ /dev/null
@@ -1,54 +0,0 @@
-#%Module######################################################################
-#
-# gcc7 modulefile 20200205
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use gcc7"
-puts stderr "The program gcc7"
-puts stderr "is added to PATH."
-}
-
-set rel [uname release]
-global prodlist
-
-#if { $rel == "2.6.32-504.16.2.el6.x86_64" } {
-# set prodlist {libc-2.14 libmpc2}
-#} else {
-# set prodlist {libmpc2}
-#}
-
-set is_module_rm [module-info mode remove]
-
-catch {set modulehomes $env(MODULEPATH)}
-#if { [ module-info mode load ] } {
-# foreach prod $prodlist {
-# foreach mfilehome [ split $modulehomes :] {
-# if { [file exists $mfilehome/$prod] } {
-# module load $prod
-# }
-# }
-# }
-#}
-#
-#if { [ module-info mode remove ] } {
-# foreach prod $prodlist {
-# foreach mfilehome [ split $modulehomes :] {
-# if { [file exists $mfilehome/$prod] } {
-# module unload $prod
-# }
-# }
-# }
-#}
-
-set GCC_LEVEL 7
-set GCC_SUBVER 0
-set GCC_CURPATH /usr/lib/gcc/x86_64-linux-gnu/
-
-prepend-path PATH $GCC_CURPATH/$GCC_LEVEL
-prepend-path LD_LIBRARY_PATH $GCC_CURPATH/$GCC_LEVEL
-setenv CPLUS_INCLUDE_PATH $GCC_CURPATH/$GCC_LEVEL/include
-setenv C_INCLUDE_PATH $GCC_CURPATH/$GCC_LEVEL/include
-
-append-path PE_PRODUCT_LIST GCC.$GCC_LEVEL
diff --git a/envfiles/gcc4.9 b/envfiles/gcc4.9
deleted file mode 100644
index 82c0204..0000000
--- a/envfiles/gcc4.9
+++ /dev/null
@@ -1,24 +0,0 @@
-#%Module######################################################################
-#
-# gcc4.9 modulefile 20160427
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use gcc4.9"
-puts stderr "The program gcc4.9"
-puts stderr "is added to PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set GCC_LEVEL 4.9
-set GCC_SUBVER 3
-set GCC_CURPATH /share/apps/bin/gcc
-
-prepend-path PATH $GCC_CURPATH/gcc-$GCC_LEVEL.$GCC_SUBVER-bin/bin
-prepend-path LD_LIBRARY_PATH $GCC_CURPATH/gcc-$GCC_LEVEL.$GCC_SUBVER-bin/lib64/:/usr/local/lib:/share/apps/lib/libmpc
-prepend-path MANPATH $GCC_CURPATH/gcc-$GCC_LEVEL.$GCC_SUBVER-bin/share/man
-
-append-path PE_PRODUCT_LIST GCC.$GCC_LEVEL
diff --git a/envfiles/gcc5.3 b/envfiles/gcc5.3
deleted file mode 100644
index 0d65d10..0000000
--- a/envfiles/gcc5.3
+++ /dev/null
@@ -1,53 +0,0 @@
-#%Module######################################################################
-#
-# gcc5.3 modulefile 20160427
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use gcc5.3"
-puts stderr "The program gcc5.3"
-puts stderr "is added to PATH."
-}
-
-set rel [uname release]
-global prodlist
-
-if { $rel == "2.6.32-504.16.2.el6.x86_64" } {
- set prodlist {libc-2.14 libmpc2}
-} else {
- set prodlist {libmpc2}
-}
-
-set is_module_rm [module-info mode remove]
-
-catch {set modulehomes $env(MODULEPATH)}
-if { [ module-info mode load ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module load $prod
- }
- }
- }
-}
-
-if { [ module-info mode remove ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module unload $prod
- }
- }
- }
-}
-
-set GCC_LEVEL 5.3
-set GCC_SUBVER 0
-set GCC_CURPATH /share/apps/bin/gcc
-
-prepend-path PATH $GCC_CURPATH/gcc-$GCC_LEVEL.$GCC_SUBVER-bin/bin
-prepend-path LD_LIBRARY_PATH $GCC_CURPATH/gcc-$GCC_LEVEL.$GCC_SUBVER-bin/lib64/:/usr/local/lib:/share/apps/lib/libmpc
-prepend-path MANPATH $GCC_CURPATH/gcc-$GCC_LEVEL.$GCC_SUBVER-bin/share/man
-
-append-path PE_PRODUCT_LIST GCC.$GCC_LEVEL
diff --git a/envfiles/gcc5.4 b/envfiles/gcc5.4
deleted file mode 100644
index 1571c51..0000000
--- a/envfiles/gcc5.4
+++ /dev/null
@@ -1,48 +0,0 @@
-#%Module######################################################################
-#
-# gcc5.4 modulefile 20160427
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use gcc5.4"
-puts stderr "The program gcc5.4"
-puts stderr "is added to PATH."
-}
-
-#global prodlist
-#set prodlist {libc-2.14 libmpc2}
-
-
-set is_module_rm [module-info mode remove]
-
-#catch {set modulehomes $env(MODULEPATH)}
-#if { [ module-info mode load ] } {
-# foreach prod $prodlist {
-# foreach mfilehome [ split $modulehomes :] {
-# if { [file exists $mfilehome/$prod] } {
-# module load $prod
-# }
-# }
-# }
-#}
-
-#if { [ module-info mode remove ] } {
-# foreach prod $prodlist {
-# foreach mfilehome [ split $modulehomes :] {
-# if { [file exists $mfilehome/$prod] } {
-# module unload $prod
-# }
-# }
-# }
-#}
-
-set GCC_LEVEL 5.4
-set GCC_SUBVER 0
-set GCC_CURPATH /share/apps/bin/gcc
-
-prepend-path PATH $GCC_CURPATH/$GCC_LEVEL/bin
-prepend-path LD_LIBRARY_PATH $GCC_CURPATH/$GCC_LEVEL/lib64/:$GCC_CURPATH/$GCC_LEVEL/lib:/usr/local/lib:/share/apps/lib/libmpc
-prepend-path MANPATH $GCC_CURPATH/gcc/share/man
-
-append-path PE_PRODUCT_LIST GCC.$GCC_LEVEL
diff --git a/envfiles/gdal-2.1.2 b/envfiles/gdal-2.1.2
index 6895926..378675b 100644
--- a/envfiles/gdal-2.1.2
+++ b/envfiles/gdal-2.1.2
@@ -14,7 +14,7 @@ set rel [uname release]
global prodlist
if { $rel != "2.6.32-504.16.2.el6.x86_64" } {
- set prodlist {libgeos-3.3.8 hdf5-1.8.9-el6 libpng-1.2.49-el6-shared}
+ set prodlist {libgeos/3.3.8 hdf5/1.8.9-el6 libpng-1.2.49-el6-shared}
} else {
set prodlist {}
}
diff --git a/envfiles/golang-1.11 b/envfiles/golang-1.11
deleted file mode 100644
index ebccadd..0000000
--- a/envfiles/golang-1.11
+++ /dev/null
@@ -1,25 +0,0 @@
-#%Module######################################################################
-#
-# golang 1.11 20190320
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use Go (golang) version 1.11"
-puts stderr "The program Go 1.11"
-puts stderr "is added to PATH."
-}
-
-set is_module_rm [module-info mode remove]
-
-unsetenv LD_LIBRARY_PATH
-set GO_LEVEL 1.11
-set GO_CURPATH /share/apps/bin/golang/$GO_LEVEL/go
-
-prepend-path PATH $GO_CURPATH/bin/
-prepend-path LD_LIBRARY_PATH $GO_CURPATH/lib/
-prepend-path MANPATH $GO_CURPATH/share/man
-setenv GOPATH ~/go
-setenv GOROOT $GO_CURPATH
-
-append-path PE_PRODUCT_LIST Golang.$GO_LEVEL
diff --git a/envfiles/golang-1.13.1 b/envfiles/golang-1.13.1
deleted file mode 100644
index 2c46a15..0000000
--- a/envfiles/golang-1.13.1
+++ /dev/null
@@ -1,31 +0,0 @@
-#%Module######################################################################
-#
-# golang 1.13 20190320
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use Go (golang) version 1.13.1"
-puts stderr "Please adjust your GOPATH because Go checker does not"
-puts stderr "like the tilde character '~'"
-puts stderr "The program Go 1.13"
-puts stderr "is added to PATH."
-}
-
-set is_module_rm [module-info mode remove]
-
-unsetenv LD_LIBRARY_PATH
-set GO_LEVEL 1.13
-set GO_SUBLVL 1
-set GO_CURPATH /share/apps/bin/golang/$GO_LEVEL.$GO_SUBLVL/go
-
-set userhome $env(HOME)
-
-prepend-path PATH $GO_CURPATH/bin/
-prepend-path LD_LIBRARY_PATH $GO_CURPATH/lib/
-prepend-path MANPATH $GO_CURPATH/share/man
-setenv GOPATH $userhome/go
-setenv GOROOT $GO_CURPATH
-setenv GO111MODULE off
-
-append-path PE_PRODUCT_LIST Golang.$GO_LEVEL.$GO_SUBLVL
diff --git a/envfiles/hdf5-1.8.18 b/envfiles/hdf5-1.8.18
deleted file mode 100644
index 322bafa..0000000
--- a/envfiles/hdf5-1.8.18
+++ /dev/null
@@ -1,26 +0,0 @@
-#%Module######################################################################
-#
-# hdf 5 1.8.18 modulefile 20170518
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use hdf5 1.8.18"
-puts stderr "The program hdf5 https://support.hdfgroup.org/HDF5/"
-puts stderr "is added to PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set HDF_LEVEL 5
-set HDF_SUBLEVEL 1.8.18
-set HDF_CURPATH /share/apps/lib/hdf$HDF_LEVEL/$HDF_SUBLEVEL
-
-prepend-path PATH $HDF_CURPATH/bin
-prepend-path LD_LIBRARY_PATH $HDF_CURPATH/lib
-prepend-path MAN_PATH $HDF_CURPATH/share/
-setenv C_INCLUDE_PATH $HDF_CURPATH/include
-setenv CPLUS_INCLUDE_PATH $HDF_CURPATH/include
-
-append-path PE_PRODUCT_LIST HDF.$HDF_LEVEL.$HDF_SUBLEVEL
diff --git a/envfiles/hdf5-1.8.9-el6 b/envfiles/hdf5-1.8.9-el6
deleted file mode 100644
index 35a699c..0000000
--- a/envfiles/hdf5-1.8.9-el6
+++ /dev/null
@@ -1,26 +0,0 @@
-#%Module######################################################################
-#
-# hdf 5 1.8.9 modulefile 20181128
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use hdf5 1.8.9"
-puts stderr "The program hdf5 https://support.hdfgroup.org/HDF5/"
-puts stderr "is added to PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set HDF_LEVEL 5
-set HDF_SUBLEVEL 1.8.9
-set HDF_CURPATH /share/apps/lib/hdf$HDF_LEVEL/$HDF_SUBLEVEL-el6-shared
-
-prepend-path PATH $HDF_CURPATH/bin
-prepend-path LD_LIBRARY_PATH $HDF_CURPATH/lib
-prepend-path MAN_PATH $HDF_CURPATH/share/
-setenv C_INCLUDE_PATH $HDF_CURPATH/include
-setenv CPLUS_INCLUDE_PATH $HDF_CURPATH/include
-
-append-path PE_PRODUCT_LIST HDF.$HDF_LEVEL.$HDF_SUBLEVEL
diff --git a/envfiles/hdf5parallel-1.8.18 b/envfiles/hdf5parallel-1.8.18
deleted file mode 100644
index 404f860..0000000
--- a/envfiles/hdf5parallel-1.8.18
+++ /dev/null
@@ -1,53 +0,0 @@
-#%Module######################################################################
-#
-# hdf 5 1.8.18 parallel version modulefile 20170518
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use hdf5 1.8.18 (parallel)"
-puts stderr "The program hdf5 https://support.hdfgroup.org/HDF5/"
-puts stderr "is added to PATH."
-}
-
-set rel [uname release]
-global prodlist
-
-if { $rel != "2.6.32-504.16.2.el6.x86_64" } {
- set prodlist {openmpi-x86_64}
-} else {
- set prodlist {}
-}
-
-set is_module_rm [module-info mode remove]
-
-catch {set modulehomes $env(MODULEPATH)}
-if { [ module-info mode load ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module load $prod
- }
- }
- }
-}
-
-if { [ module-info mode remove ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module unload $prod
- }
- }
- }
-}
-
-set HDF_LEVEL 5
-set HDF_SUBLEVEL 1.8.18
-set HDF_CURPATH /share/apps/lib/hdf$HDF_LEVEL/$HDF_SUBLEVEL/parallel
-
-prepend-path PATH $HDF_CURPATH/bin
-prepend-path LD_LIBRARY_PATH $HDF_CURPATH/lib
-prepend-path MAN_PATH $HDF_CURPATH/share/
-
-append-path PE_PRODUCT_LIST HDF.$HDF_LEVEL.$HDF_SUBLEVEL-parallel
diff --git a/envfiles/libgeos-3.3.8 b/envfiles/libgeos-3.3.8
deleted file mode 100644
index 878f4a7..0000000
--- a/envfiles/libgeos-3.3.8
+++ /dev/null
@@ -1,22 +0,0 @@
-#%Module######################################################################
-#
-# libgeos3.3.8 modulefile 20181127
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use the library libgeos3"
-puts stderr "The library libgeos3"
-puts stderr "is added to your LD_LIBRARY_PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set LIBGEOS_LVL 3
-set LIBGEOS_SUBVER 3.8
-set LIBGEOS_CURPATH /share/apps/lib/geos/$LIBGEOS_LVL.$LIBGEOS_SUBVER
-
-prepend-path LD_LIBRARY_PATH $LIBGEOS_CURPATH/
-
-append-path PE_PRODUCT_LIST LIBGEOS.$LIBGEOS_LVL.$LIBGEOS_SUBVER
diff --git a/envfiles/libgeos_c-1.7.8 b/envfiles/libgeos_c-1.7.8
deleted file mode 100644
index daa925e..0000000
--- a/envfiles/libgeos_c-1.7.8
+++ /dev/null
@@ -1,22 +0,0 @@
-#%Module######################################################################
-#
-# libgeos3.3.8 modulefile 20181127
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use the library libgeos3"
-puts stderr "The library libgeos3"
-puts stderr "is added to your LD_LIBRARY_PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set LIBGEOSC_LVL 1
-set LIBGEOSC_SUBVER 7.8
-set LIBGEOSC_CURPATH /share/apps/lib/geos/geos_c/$LIBGEOSC_LVL.$LIBGEOSC_SUBVER
-
-prepend-path LD_LIBRARY_PATH $LIBGEOSC_CURPATH/
-
-append-path PE_PRODUCT_LIST LIBGEOSC.$LIBGEOSC_LVL.$LIBGEOSC_SUBVER
\ No newline at end of file
diff --git a/envfiles/libz-1.2.11 b/envfiles/libz-1.2.11
deleted file mode 100644
index 469319b..0000000
--- a/envfiles/libz-1.2.11
+++ /dev/null
@@ -1,23 +0,0 @@
-#%Module######################################################################
-#
-# zlib 1.2.11 modulefile 201701111
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use the library zlib 1.2.11"
-puts stderr "The library zlib"
-puts stderr "is added to your LD_LIBRARY_PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set ZLIB_LEVEL 1.2
-set ZLIB_SUBVER 11
-set ZLIB_CURPATH /share/apps/lib/libz/
-
-prepend-path LD_LIBRARY_PATH $ZLIB_CURPATH/$ZLIB_LEVEL.$ZLIB_SUBVER/lib/
-
-append-path PE_PRODUCT_LIST ZLIB
-
diff --git a/envfiles/libz-1.2.6 b/envfiles/libz-1.2.6
deleted file mode 100644
index dfdf25d..0000000
--- a/envfiles/libz-1.2.6
+++ /dev/null
@@ -1,23 +0,0 @@
-#%Module######################################################################
-#
-# zlib 1.2.6 modulefile 20170118
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use the library zlib 1.2.6"
-puts stderr "The library zlib"
-puts stderr "is added to your LD_LIBRARY_PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set ZLIB_LEVEL 1.2
-set ZLIB_SUBVER 6
-set ZLIB_CURPATH /share/apps/lib/libz/
-
-prepend-path LD_LIBRARY_PATH $ZLIB_CURPATH/$ZLIB_LEVEL.$ZLIB_SUBVER/
-
-append-path PE_PRODUCT_LIST ZLIB
-
diff --git a/envfiles/libz-1.2.8 b/envfiles/libz-1.2.8
deleted file mode 100644
index c1c9dbc..0000000
--- a/envfiles/libz-1.2.8
+++ /dev/null
@@ -1,46 +0,0 @@
-#%Module######################################################################
-#
-# zlib 1.2.8 modulefile 20170118
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use the library zlib 1.2.8"
-puts stderr "The library zlib"
-puts stderr "is added to your LD_LIBRARY_PATH."
-}
-
-set prodlist { libc2.14 }
-
-set is_module_rm [module-info mode remove]
-
-catch {set modulehomes $env(MODULEPATH)}
-
-if { [ module-info mode load ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module load $prod
- }
- }
- }
-}
-if { [ module-info mode remove ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module unload $prod
- }
- }
- }
-}
-
-
-set ZLIB_LEVEL 1.2
-set ZLIB_SUBVER 8
-set ZLIB_CURPATH /share/apps/lib/libz/
-
-prepend-path LD_LIBRARY_PATH $ZLIB_CURPATH/$ZLIB_LEVEL.$ZLIB_SUBVER/lib/
-
-append-path PE_PRODUCT_LIST ZLIB
-
diff --git a/envfiles/netcdf-4.3.3.1 b/envfiles/netcdf-4.3.3.1
deleted file mode 100644
index c6f314c..0000000
--- a/envfiles/netcdf-4.3.3.1
+++ /dev/null
@@ -1,22 +0,0 @@
-#%Module######################################################################
-#
-# netcdf 4.3.3.1 modulefile 20170518
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use netcdf 4.3.3.1"
-puts stderr "The program netcdf https://www.unidata.ucar.edu/downloads/netcdf/index.jsp"
-puts stderr "is added to PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set NCDF_LEVEL 4.3.3.1
-set NCDF_CURPATH /share/apps/lib/netcdf-$NCDF_LEVEL
-
-prepend-path PATH $NCDF_CURPATH/:$NCDF_CURPATH/ncdump:$NCDF_CURPATH/:$NCDF_CURPATH/ncgen:$NCDF_CURPATH/:$NCDF_CURPATH/ncgen3:$NCDF_CURPATH/nctest:$NCDF_CURPATH/nc_test:$NCDF_CURPATH/nc_test4:$NCDF_CURPATH/ncdap_test:$NCDF_CURPATH/h5_test
-prepend-path LD_LIBRARY_PATH $NCDF_CURPATH/:$NCDF_CURPATH/liblib:$NCDF_CURPATH/libldap2:$NCDF_CURPATH/libdispatch:$NCDF_CURPATH/libsrc:$NCDF_CURPATH/libsrc4:$NCDF_CURPATH/libsrc5
-
-append-path PE_PRODUCT_LIST NETCDF.$NCDF_LEVEL
diff --git a/envfiles/netcdf-4.4.1.1 b/envfiles/netcdf-4.4.1.1
deleted file mode 100644
index b6a632b..0000000
--- a/envfiles/netcdf-4.4.1.1
+++ /dev/null
@@ -1,23 +0,0 @@
-#%Module######################################################################
-#
-# netcdf 4.4.1.1 modulefile 20170518
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use netcdf 4.4.1.1"
-puts stderr "The program netcdf https://www.unidata.ucar.edu/downloads/netcdf/index.jsp"
-puts stderr "is added to PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set NCDF_LEVEL 4.4.1.1
-set NCDF_CURPATH /share/apps/lib/netcdf/$NCDF_LEVEL
-
-prepend-path PATH $NCDF_CURPATH/bin
-prepend-path LD_LIBRARY_PATH $NCDF_CURPATH/lib
-prepend-path MAN_PATH $NCDF_CURPATH/share/man
-
-append-path PE_PRODUCT_LIST NETCDF.$NCDF_LEVEL
diff --git a/envfiles/openmpi-4.0.1 b/envfiles/openmpi-4.0.1
index 91f7c79..c486791 100644
--- a/envfiles/openmpi-4.0.1
+++ b/envfiles/openmpi-4.0.1
@@ -26,7 +26,7 @@ global prodlist
conflict openmpi
if { $rel != "2.6.32-504.16.2.el6.x86_64" } {
- set prodlist {dapl1.2}
+ set prodlist {dapl/1.2}
} else {
set prodlist {}
}
diff --git a/envfiles/openssl-1.1.0b b/envfiles/openssl-1.1.0b
deleted file mode 100644
index 5fde3bf..0000000
--- a/envfiles/openssl-1.1.0b
+++ /dev/null
@@ -1,24 +0,0 @@
-#%Module######################################################################
-#
-# openssl 1.1.0b modulefile 20161014
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use OpenSSL"
-puts stderr "The program OpenSSL"
-puts stderr "is added to PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set OPENSSL_LEVEL 1.1
-set OPENSSL_SUBVER 0b
-set OPENSSL_CURPATH /share/apps/lib/openssl
-
-prepend-path PATH $OPENSSL_CURPATH/$OPENSSL_LEVEL.$OPENSSL_SUBVER/bin
-prepend-path LD_LIBRARY_PATH $OPENSSL_CURPATH/$OPENSSL_LEVEL.$OPENSSL_SUBVER/lib
-prepend-path MANPATH $OPENSSL_CURPATH/$OPENSSL_LEVEL.$OPENSSL_SUBVER/share/man
-
-append-path PE_PRODUCT_LIST OPENSSL
diff --git a/envfiles/openssl-3.0.0 b/envfiles/openssl-3.0.0
deleted file mode 100644
index 5944ed4..0000000
--- a/envfiles/openssl-3.0.0
+++ /dev/null
@@ -1,24 +0,0 @@
-#%Module######################################################################
-#
-# openssl 3.0.0 (following 1.1.1) modulefile 20191023
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use OpenSSL"
-puts stderr "The program OpenSSL"
-puts stderr "is added to PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set OPENSSL_LEVEL 3.0
-set OPENSSL_SUBVER 0
-set OPENSSL_CURPATH /share/apps/lib/openssl
-
-prepend-path PATH $OPENSSL_CURPATH/$OPENSSL_LEVEL.$OPENSSL_SUBVER/bin
-prepend-path LD_LIBRARY_PATH $OPENSSL_CURPATH/$OPENSSL_LEVEL.$OPENSSL_SUBVER/lib
-prepend-path MANPATH $OPENSSL_CURPATH/$OPENSSL_LEVEL.$OPENSSL_SUBVER/share/man
-
-append-path PE_PRODUCT_LIST OPENSSL.$OPENSSL_LEVEL.$OPENSSL_SUBVER
diff --git a/envfiles/openssl-devel-1.0.1e b/envfiles/openssl-devel-1.0.1e
deleted file mode 100644
index f3c29ec..0000000
--- a/envfiles/openssl-devel-1.0.1e
+++ /dev/null
@@ -1,33 +0,0 @@
-#%Module######################################################################
-#
-# openssl 1.0.1e modulefile 20190315
-# from http://rpmfind.net/linux/centos/6.10/os/x86_64/Packages/openssl-devel-1.0.1e-57.el6.x86_64.rpm
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use OpenSSL-devel 1.0.1e"
-puts stderr "The program OpenSSL"
-puts stderr "is added to PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set OPENSSL_LEVEL 1.0.1
-set OPENSSL_SUBVER e
-set OPENSSL_CURPATH /share/apps/lib/openssl
-
-prepend-path LD_LIBRARY_PATH $OPENSSL_CURPATH/$OPENSSL_LEVEL$OPENSSL_SUBVER/lib64
-prepend-path MANPATH $OPENSSL_CURPATH/$OPENSSL_LEVEL$OPENSSL_SUBVER/share/man
-
-prepend-path --delim " " C_INCLUDE_PATH -I$OPENSSL_CURPATH/$OPENSSL_LEVEL$OPENSSL_SUBVER/include
-prepend-path --delim " " CPLUS_INCLUDE_PATH -I$OPENSSL_CURPATH/$OPENSSL_LEVEL$OPENSSL_SUBVER/include
-
-prepend-path --delim " " CGO_LDFLAGS -L$OPENSSL_CURPATH/$OPENSSL_LEVEL$OPENSSL_SUBVER/lib64
-prepend-path --delim " " CGO_CFLAGS -I$OPENSSL_CURPATH/$OPENSSL_LEVEL$OPENSSL_SUBVER/include
-
-prepend-path --delim " " LDFLAGS -L$OPENSSL_CURPATH/$OPENSSL_LEVEL$OPENSSL_SUBVER/lib64
-prepend-path --delim " " CFLAGS -I$OPENSSL_CURPATH/$OPENSSL_LEVEL$OPENSSL_SUBVER/include
-
-
-append-path PE_PRODUCT_LIST OPENSSL-$OPENSSL_LEVEL$OPENSSL_SUBVER
diff --git a/envfiles/samtools0.1.19 b/envfiles/samtools0.1.19
deleted file mode 100644
index 9f4c143..0000000
--- a/envfiles/samtools0.1.19
+++ /dev/null
@@ -1,24 +0,0 @@
-#%Module######################################################################
-#
-# samtools 0.1.19 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use samtools 0.1.19"
-puts stderr "The program samtools 0.1.19"
-puts stderr "is added to PATH."
-}
-
-set is_module_rm [module-info mode remove]
-
-unsetenv LD_LIBRARY_PATH
-set SAMTOOLS_LEVEL 0.1.19
-set SAMTOOLS_CURPATH /share/apps/bin/samtools-0.1.19/
-
-prepend-path PATH $SAMTOOLS_CURPATH/
-#prepend-path LD_LIBRARY_PATH /usr/local/lib
-#prepend-path LD_LIBRARY_PATH /usr/lib64
-setenv LD_LIBRARY_PATH /usr/lib64:/usr/local/lib:/opt/gridengine/lib/linux-x64:/opt/openmpi/lib:/lib64:/usr/local/lib64:/usr/lib/:/opt/python/lib
-
-append-path PE_PRODUCT_LIST SAMTOOLS
diff --git a/envfiles/samtools1.3 b/envfiles/samtools1.3
deleted file mode 100644
index 5e62713..0000000
--- a/envfiles/samtools1.3
+++ /dev/null
@@ -1,54 +0,0 @@
-#%Module######################################################################
-#
-# samtools 1.3 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use samtools 1.3"
-puts stderr "The program samtools 1.3"
-puts stderr "is added to PATH."
-}
-
-unsetenv LD_LIBRARY_PATH
-set SAMTOOLS_LEVEL 1.3
-set SAMTOOLS_CURPATH /share/apps/bin/samtools-1.3
-
-set rel [uname release]
-global prodlist
-
-if { $rel == "2.6.32-504.16.2.el6.x86_64" } {
- set prodlist {libz-1.2.8 libc-2.14}
-} else {
- set prodlist {libz-1.2.8}
-}
-
-set is_module_rm [module-info mode remove]
-
-catch {set modulehomes $env(MODULEPATH)}
-if { [ module-info mode load ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module load $prod
- }
- }
- }
-}
-
-if { [ module-info mode remove ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module unload $prod
- }
- }
- }
-}
-set is_module_rm [module-info mode remove]
-
-prepend-path PATH $SAMTOOLS_CURPATH/bin
-#setenv LD_LIBRARY_PATH /usr/lib64:/usr/local/lib:/opt/gridengine/lib/linux-x64:/opt/openmpi/lib:/lib64:/usr/local/lib64:/usr/lib/:/opt/python/lib
-prepend-path MANPATH $SAMTOOLS_CURPATH/share/man
-
-append-path PE_PRODUCT_LIST SAMTOOLS
diff --git a/envfiles/singularity-2.4.1 b/envfiles/singularity-2.4.1
deleted file mode 100644
index 1818524..0000000
--- a/envfiles/singularity-2.4.1
+++ /dev/null
@@ -1,23 +0,0 @@
-#%Module######################################################################
-#
-# singularity 2.4.1 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use singularity 2.4.1"
-puts stderr "The program singularity 2.4.1"
-puts stderr "is added to PATH."
-}
-
-set is_module_rm [module-info mode remove]
-
-unsetenv LD_LIBRARY_PATH
-set SING_LEVEL 2.4.1
-set SING_CURPATH /share/apps/bin/singularity/$SING_LEVEL/
-
-prepend-path PATH $SING_CURPATH/bin/
-prepend-path LD_LIBRARY_PATH $SING_CURPATH/lib/
-prepend-path MANPATH $SING_CURPATH/share/man
-
-append-path PE_PRODUCT_LIST Singularity.$SING_LEVEL
diff --git a/envfiles/singularity-2.6 b/envfiles/singularity-2.6
deleted file mode 100644
index 7a889bf..0000000
--- a/envfiles/singularity-2.6
+++ /dev/null
@@ -1,23 +0,0 @@
-#%Module######################################################################
-#
-# singularity 2.6 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use singularity 2.6"
-puts stderr "The program singularity 2.6"
-puts stderr "is added to PATH."
-}
-
-set is_module_rm [module-info mode remove]
-
-unsetenv LD_LIBRARY_PATH
-set SING_LEVEL 2.6
-set SING_CURPATH /share/apps/bin/singularity/$SING_LEVEL/
-
-prepend-path PATH $SING_CURPATH/bin/
-prepend-path LD_LIBRARY_PATH $SING_CURPATH/lib/
-prepend-path MANPATH $SING_CURPATH/share/man
-
-append-path PE_PRODUCT_LIST Singularity.$SING_LEVEL
diff --git a/envfiles/singularity-3.1 b/envfiles/singularity-3.1
deleted file mode 100644
index d6d1eff..0000000
--- a/envfiles/singularity-3.1
+++ /dev/null
@@ -1,25 +0,0 @@
-#%Module######################################################################
-#
-# singularity 3.1 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use singularity 3.1"
-puts stderr "The program singularity 3.1"
-puts stderr "is added to PATH."
-}
-
-set is_module_rm [module-info mode remove]
-
-unsetenv LD_LIBRARY_PATH
-set SING_LEVEL 3.1
-set SING_CURPATH /share/apps/bin/singularity/$SING_LEVEL/
-set SING_IMG /share/apps/sing-images/$SING_LEVEL/
-
-prepend-path PATH $SING_CURPATH/bin/
-prepend-path PATH $SING_IMG
-prepend-path LD_LIBRARY_PATH $SING_CURPATH/lib/
-prepend-path MANPATH $SING_CURPATH/share/man
-
-append-path PE_PRODUCT_LIST Singularity.$SING_LEVEL
diff --git a/envfiles/singularity-3.4.2 b/envfiles/singularity-3.4.2
deleted file mode 100644
index 165e34a..0000000
--- a/envfiles/singularity-3.4.2
+++ /dev/null
@@ -1,25 +0,0 @@
-#%Module######################################################################
-#
-# 20191028 singularity 3.4.2 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use singularity 3.4.2"
-puts stderr "The program singularity 3.4.2"
-puts stderr "is added to PATH."
-}
-
-set is_module_rm [module-info mode remove]
-
-unsetenv LD_LIBRARY_PATH
-set SING_LEVEL 3.4.2
-set SING_CURPATH /share/apps/bin/singularity/$SING_LEVEL/
-set SING_IMG /share/apps/sing-images/$SING_LEVEL/
-
-prepend-path PATH $SING_CURPATH/bin/
-prepend-path PATH $SING_IMG
-prepend-path LD_LIBRARY_PATH $SING_CURPATH/lib/
-prepend-path MANPATH $SING_CURPATH/share/man
-
-append-path PE_PRODUCT_LIST Singularity.$SING_LEVEL
diff --git a/envfiles/stacks1.37 b/envfiles/stacks1.37
deleted file mode 100644
index c6565d1..0000000
--- a/envfiles/stacks1.37
+++ /dev/null
@@ -1,25 +0,0 @@
-#%Module######################################################################
-#
-# stacks 1.37 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use stacks 1.37"
-puts stderr "The program stacks 1.37 [ustacks, pstacks, cstacks, estacks, sstacks ...]"
-puts stderr "is added to PATH."
-}
-
-set is_module_rm [module-info mode remove]
-
-unsetenv LD_LIBRARY_PATH
-set STACKS_LEVEL 1.37
-set STACKS_CURPATH /share/apps/bin/stacks-$STACKS_LEVEL/
-
-prepend-path PATH $STACKS_CURPATH/bin/
-#prepend-path LD_LIBRARY_PATH /usr/local/lib
-#prepend-path LD_LIBRARY_PATH /usr/lib64
-setenv LD_LIBRARY_PATH /usr/lib64:/usr/local/lib:/opt/gridengine/lib/linux-x64:/opt/openmpi/lib:/lib64:/usr/local/lib64:/usr/lib/:/opt/python/lib
-prepend-path MANPATH $STACKS_CURPATH/man
-
-append-path PE_PRODUCT_LIST STACKS
diff --git a/envfiles/stacks1.40 b/envfiles/stacks1.40
deleted file mode 100644
index 7762274..0000000
--- a/envfiles/stacks1.40
+++ /dev/null
@@ -1,25 +0,0 @@
-#%Module######################################################################
-#
-# stacks 1.40 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use stacks 1.40"
-puts stderr "The program stacks 1.40 [ustacks, pstacks, cstacks, estacks, sstacks ...]"
-puts stderr "is added to PATH."
-}
-
-set is_module_rm [module-info mode remove]
-
-unsetenv LD_LIBRARY_PATH
-set STACKS_LEVEL 1.40
-set STACKS_CURPATH /share/apps/bin/stacks-$STACKS_LEVEL/
-
-prepend-path PATH $STACKS_CURPATH/bin/
-#prepend-path LD_LIBRARY_PATH /usr/local/lib
-#prepend-path LD_LIBRARY_PATH /usr/lib64
-setenv LD_LIBRARY_PATH /share/apps/bin/gcc/gcc-5.3.0-bin/lib64/:/usr/lib64:/usr/local/lib:/opt/gridengine/lib/linux-x64:/opt/openmpi/lib:/lib64:/usr/local/lib64:/usr/lib/:/opt/python/lib
-prepend-path MANPATH $STACKS_CURPATH/man
-
-append-path PE_PRODUCT_LIST STACKS
diff --git a/envfiles/stacks1.46 b/envfiles/stacks1.46
deleted file mode 100644
index 14afe83..0000000
--- a/envfiles/stacks1.46
+++ /dev/null
@@ -1,51 +0,0 @@
-#%Module######################################################################
-#
-# stacks 1.40 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use stacks 1.46"
-puts stderr "The program stacks 1.46 [ustacks, pstacks, cstacks, estacks, sstacks ...]"
-puts stderr "is added to PATH."
-}
-
-set rel [uname release]
-global prodlist
-
-if { $rel == "2.6.32-504.16.2.el6.x86_64" } {
- set prodlist {gcc4.9 libz-1.2.8 \
- libc-2.14}
-}
-
-set is_module_rm [module-info mode remove]
-
-catch {set modulehomes $env(MODULEPATH)}
-if { [ module-info mode load ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module load $prod
- }
- }
- }
-}
-
-if { [ module-info mode remove ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module unload $prod
- }
- }
- }
-}
-
-
-set STACKS_LEVEL 1.46
-set STACKS_CURPATH /share/apps/bin/stacks-$STACKS_LEVEL/
-
-prepend-path PATH $STACKS_CURPATH/bin/
-prepend-path MANPATH $STACKS_CURPATH/man
-
-append-path PE_PRODUCT_LIST STACKS.$STACKS_LEVEL
diff --git a/envfiles/stacks1.48 b/envfiles/stacks1.48
deleted file mode 100644
index 34b56fb..0000000
--- a/envfiles/stacks1.48
+++ /dev/null
@@ -1,51 +0,0 @@
-#%Module######################################################################
-#
-# stacks 1.48 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use stacks 1.48"
-puts stderr "The program stacks 1.48 [ustacks, pstacks, cstacks, estacks, sstacks ...]"
-puts stderr "is added to PATH."
-}
-
-set rel [uname release]
-global prodlist
-
-if { $rel == "2.6.32-504.16.2.el6.x86_64" } {
- set prodlist {gcc4.9 libz-1.2.8 \
- libc-2.14}
-}
-
-set is_module_rm [module-info mode remove]
-
-catch {set modulehomes $env(MODULEPATH)}
-if { [ module-info mode load ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module load $prod
- }
- }
- }
-}
-
-if { [ module-info mode remove ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module unload $prod
- }
- }
- }
-}
-
-
-set STACKS_LEVEL 1.48
-set STACKS_CURPATH /share/apps/bin/stacks/$STACKS_LEVEL/
-
-prepend-path PATH $STACKS_CURPATH/bin/
-prepend-path MANPATH $STACKS_CURPATH/man
-
-append-path PE_PRODUCT_LIST STACKS.$STACKS_LEVEL
diff --git a/envfiles/stacks2.0beta b/envfiles/stacks2.0beta
deleted file mode 100644
index 009d5a8..0000000
--- a/envfiles/stacks2.0beta
+++ /dev/null
@@ -1,51 +0,0 @@
-#%Module######################################################################
-#
-# stacks 2.0 beta modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use stacks 2.0 beta"
-puts stderr "The program stacks 2.0 [ustacks, pstacks, cstacks, estacks, sstacks ...]"
-puts stderr "is added to PATH."
-}
-
-set rel [uname release]
-global prodlist
-
-if { $rel == "2.6.32-504.16.2.el6.x86_64" } {
- set prodlist {gcc4.9 libz-1.2.8 \
- libc-2.14}
-}
-
-set is_module_rm [module-info mode remove]
-
-catch {set modulehomes $env(MODULEPATH)}
-if { [ module-info mode load ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module load $prod
- }
- }
- }
-}
-
-if { [ module-info mode remove ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module unload $prod
- }
- }
- }
-}
-
-
-set STACKS_LEVEL 2.0_Beta
-set STACKS_CURPATH /share/apps/bin/stacks/$STACKS_LEVEL/
-
-prepend-path PATH $STACKS_CURPATH/bin/
-prepend-path MANPATH $STACKS_CURPATH/man
-
-append-path PE_PRODUCT_LIST STACKS.$STACKS_LEVEL
diff --git a/envfiles/stacks2.0beta.10a b/envfiles/stacks2.0beta.10a
deleted file mode 100644
index 3fe6ff5..0000000
--- a/envfiles/stacks2.0beta.10a
+++ /dev/null
@@ -1,52 +0,0 @@
-#%Module######################################################################
-#
-# stacks 2.0 beta modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use stacks 2.0 beta 10a"
-puts stderr "The program stacks 2.0 [ustacks, pstacks, cstacks, estacks, sstacks ...]"
-puts stderr "is added to PATH."
-}
-
-set rel [uname release]
-global prodlist
-
-if { $rel == "2.6.32-504.16.2.el6.x86_64" } {
- set prodlist {gcc4.9 libz-1.2.8 \
- libc-2.14}
-}
-
-set is_module_rm [module-info mode remove]
-
-catch {set modulehomes $env(MODULEPATH)}
-if { [ module-info mode load ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module load $prod
- }
- }
- }
-}
-
-if { [ module-info mode remove ] } {
- foreach prod $prodlist {
- foreach mfilehome [ split $modulehomes :] {
- if { [file exists $mfilehome/$prod] } {
- module unload $prod
- }
- }
- }
-}
-
-
-set STACKS_LEVEL 2.0_Beta
-set STACKS_SUBLEVEL 10a
-set STACKS_CURPATH /share/apps/bin/stacks/$STACKS_LEVEL/$STACKS_SUBLEVEL
-
-prepend-path PATH $STACKS_CURPATH/bin/
-prepend-path MANPATH $STACKS_CURPATH/man
-
-append-path PE_PRODUCT_LIST STACKS.$STACKS_LEVEL.$STACKS_SUBLEVEL
diff --git a/envfiles/tabix-0.2.6 b/envfiles/tabix-0.2.6
index fd27803..954db5b 100644
--- a/envfiles/tabix-0.2.6
+++ b/envfiles/tabix-0.2.6
@@ -12,7 +12,7 @@ puts stderr "is added to PATH."
set rel [uname release]
global prodlist
-set prodlist {libz-1.2.11}
+set prodlist {libz/1.2.11}
set is_module_rm [module-info mode remove]
diff --git a/envfiles/vcftools-0.1.15 b/envfiles/vcftools-0.1.15
index 89a83eb..ef3245b 100644
--- a/envfiles/vcftools-0.1.15
+++ b/envfiles/vcftools-0.1.15
@@ -15,8 +15,8 @@ global prodlist
if { $rel == "2.6.32-504.16.2.el6.x86_64" } {
# libz does not seem to be mandatory
- set prodlist {gcc4.9 libc-2.14 \
- libz-1.2.11 }
+ set prodlist {gcc/4.9 libc/2.14 \
+ libz/1.2.11 }
}
set is_module_rm [module-info mode remove]
--
GitLab