Commit 1a23ad0a authored by remy's avatar remy
Browse files

adding samtools/htslib/tabix/bcftools 1.10

parent 9f1b16d0
#%Module######################################################################
#
# 20200224 bcftools-1.10 modulefile
#
proc ModulesHelp { } {
puts stderr "This modulefile defines the library paths and"
puts stderr "include paths needed to use bcftools1.10"
puts stderr "The program bcftools/1.10"
puts stderr "is added to PATH."
}
set rel [uname release]
global prodlist
set prodlist {htslib/1.10.2 curl/7.68.0-dev}
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 $prod
}
}
}
}
set BCFT_LVL 1.10
set BCFT_CURPATH /share/apps/bin/bcftools/$BCFT_LVL
prepend-path PATH $BCFT_CURPATH/bin/
prepend-path LD_LIBRARY_PATH $BCFT_CURPATH/libexec
prepend-path MANPATH $BCFT_CURPATH/share/man
append-path PE_PRODUCT_LIST BCFTOOLS.$BCFT_LVL
#%Module######################################################################
#
# 20200224 htslib-1.2.1 modulefile
#
proc ModulesHelp { } {
puts stderr "This modulefile defines the library paths and"
puts stderr "include paths needed to use htslib-1.10.2"
puts stderr "The program htslib-1.10.2"
puts stderr "is added to PATH."
}
set rel [uname release]
set is_module_rm [module-info mode remove]
set HTSLIB_LVL 1.10.2
set HTSLIB_CURPATH /share/apps/lib/htslib/$HTSLIB_LVL/usr/local
setenv C_INCLUDE_PATH $HTSLIB_CURPATH/include
setenv CPLUS_INCLUDE_PATH $HTSLIB_CURPATH/include
prepend-path PATH $HTSLIB_CURPATH/bin
prepend-path LD_LIBRARY_PATH $HTSLIBL_CURPATH/lib
prepend-path MANPATH $HTSLIB_CURPATH/share/man
append-path PE_PRODUCT_LIST HTSLIB.$HTSLIB_LVL
#%Module######################################################################
#
# 20200224 samtools 1.10 modulefile
#
proc ModulesHelp { } {
puts stderr "This modulefile defines the library paths and"
puts stderr "include paths needed to use samtools 1.10"
puts stderr "The program samtools 1.10"
puts stderr "is added to PATH."
}
unsetenv LD_LIBRARY_PATH
set SAMTOOLS_LEVEL 1.10
set SAMTOOLS_CURPATH /share/apps/bin/samtools/1.10
set rel [uname release]
global prodlist
set prodlist {htslib/1.10.2 bcftools/1.10}
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
#%Module######################################################################
#
# tabix 0.2.6 modulefile
#
proc ModulesHelp { } {
puts stderr "This modulefile defines the library paths and"
puts stderr "include paths needed to use tabix-0.2.6"
puts stderr "The program tabix-0.2.6"
puts stderr "is added to PATH."
}
set rel [uname release]
global prodlist
set prodlist {libz/1.2.11}
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 $prod
}
}
}
}
set TABX_LVL 0.2.6
set TBX_CURPATH /share/apps/bin/tabix/$TABX_LVL
prepend-path PATH $TBX_CURPATH/
append-path PE_PRODUCT_LIST TABIX.$TABX_LVL
#%Module######################################################################
#
# 20200224 tabix 1.10.2 modulefile
#
proc ModulesHelp { } {
puts stderr "This modulefile defines the library paths and"
puts stderr "include paths needed to use tabix1.10.2"
puts stderr "The program tabix/1.10.2"
puts stderr "is added to PATH."
}
set rel [uname release]
global prodlist
set prodlist {htslib/1.10.2}
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 $prod
}
}
}
}
set TABX_LVL 1.10.2
append-path PE_PRODUCT_LIST TABIX.$TABX_LVL
#%Module######################################################################
#
# 20200224 tabix 1.2.1 modulefile
#
proc ModulesHelp { } {
puts stderr "This modulefile defines the library paths and"
puts stderr "include paths needed to use tabix1.2.1"
puts stderr "The program tabix/1.2.1"
puts stderr "is added to PATH."
}
set rel [uname release]
global prodlist
set prodlist {htslib/1.2.1}
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 $prod
}
}
}
}
set TABX_LVL 1.2.1
append-path PE_PRODUCT_LIST TABIX.$TABX_LVL
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