reorganize + go /home/dernatremy to set GOPATH

2ccdb544 · remy · 46e03b37 · 46e03b37 · 46e03b37 · 46e03b37
Commit 2ccdb544 authored Feb 21, 2020 by remy
--- a/envfiles/R-3.0.3
+++ b/envfiles/R-3.0.3
-#%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    $R_CURPATH/lib64/R/library
--- a/envfiles/R-3.1.3
+++ b/envfiles/R-3.1.3
-#%Module######################################################################
-#
-# R-3.1.3 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use R-3.1.3"
-puts stderr "The program R-3.1.3"
-puts stderr "is added to PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set R_LEVEL 3.1.3
-set R_CURPATH /share/apps/bin/R/R-$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    $R_CURPATH/lib64/R/library
--- a/envfiles/R-3.2.0
+++ b/envfiles/R-3.2.0
-#%Module######################################################################
-#
-# R-3.2.0 modulefile
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use R-3.2.0"
-puts stderr "The program R-3.2.0"
-puts stderr "is added to PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set R_LEVEL 3.2.0
-set R_CURPATH /share/apps/bin/R/R-$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
--- a/envfiles/R-3.3.1
+++ b/envfiles/R-3.3.1
-#%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
--- a/envfiles/R-3.4.3
+++ b/envfiles/R-3.4.3
-#%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
--- a/envfiles/R-3.5.3
+++ b/envfiles/R-3.5.3
-#%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
--- a/envfiles/R-343-jags
+++ b/envfiles/R-343-jags
-#%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
--- 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]

--- 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]


--- 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]

--- 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]


--- a/envfiles/blast-2.6.0
+++ b/envfiles/blast-2.6.0
-#%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
--- a/envfiles/blast-2.8.1
+++ b/envfiles/blast-2.8.1
-#%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
--- 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]


--- a/envfiles/dapl1.2
+++ b/envfiles/dapl1.2
-#%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.$LIBDAPL_SUBVER
--- a/envfiles/dapl2
+++ b/envfiles/dapl2
-#%Module######################################################################
-#
-# libdapl 2.0.34 modulefile 20181127
-#
-
-proc ModulesHelp { } {
-puts stderr "This modulefile defines the library paths and"
-puts stderr "include paths needed to use the library lib dapl 1.2"
-puts stderr "The library dapl1.2 - The DAT API library https://www.openfabrics.org/"
-puts stderr "is added to your LD_LIBRARY_PATH."
-}
-
-
-set is_module_rm [module-info mode remove]
-
-set LIBDAPL_LVL 2
-set LIBDAPL_SUBVER 0.34
-set LIBDAPL_CURPATH /share/apps/lib/dapl/$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
--- 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 {}
 }

--- 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]


--- a/envfiles/gcc-current-7
+++ b/envfiles/gcc-current-7
-#%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
--- a/envfiles/gcc4.9
+++ b/envfiles/gcc4.9
-#%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