diff --git a/envfiles/bcftools/1.10 b/envfiles/bcftools/1.10 new file mode 100644 index 0000000000000000000000000000000000000000..53765b8fadaebd0d4f5f98c60f6d8952d5cfcf05 --- /dev/null +++ b/envfiles/bcftools/1.10 @@ -0,0 +1,49 @@ +#%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 diff --git a/envfiles/bcftools-1.3 b/envfiles/bcftools/1.3 similarity index 100% rename from envfiles/bcftools-1.3 rename to envfiles/bcftools/1.3 diff --git a/envfiles/htslib/1.10.2 b/envfiles/htslib/1.10.2 new file mode 100644 index 0000000000000000000000000000000000000000..47ace01ba0eec15ae35222aebdbc60fbdf112da3 --- /dev/null +++ b/envfiles/htslib/1.10.2 @@ -0,0 +1,27 @@ +#%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 diff --git a/envfiles/htslib-1.2.1 b/envfiles/htslib/1.2.1 similarity index 100% rename from envfiles/htslib-1.2.1 rename to envfiles/htslib/1.2.1 diff --git a/envfiles/samtools/1.10 b/envfiles/samtools/1.10 new file mode 100644 index 0000000000000000000000000000000000000000..98a452c65cae05529fe500847d9049936daa5f8d --- /dev/null +++ b/envfiles/samtools/1.10 @@ -0,0 +1,50 @@ +#%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 diff --git a/envfiles/tabix/0.2.6 b/envfiles/tabix/0.2.6 new file mode 100644 index 0000000000000000000000000000000000000000..78a400eed192577a3447e327275658632f7e2ee0 --- /dev/null +++ b/envfiles/tabix/0.2.6 @@ -0,0 +1,47 @@ +#%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 diff --git a/envfiles/tabix/1.10.2 b/envfiles/tabix/1.10.2 new file mode 100644 index 0000000000000000000000000000000000000000..1144cab88b66c0434a5b47e6b723c2248f167a9c --- /dev/null +++ b/envfiles/tabix/1.10.2 @@ -0,0 +1,44 @@ +#%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 diff --git a/envfiles/tabix/1.2.1 b/envfiles/tabix/1.2.1 new file mode 100644 index 0000000000000000000000000000000000000000..4035e082ccf0821ad3b9573abf5fe30eb245443e --- /dev/null +++ b/envfiles/tabix/1.2.1 @@ -0,0 +1,44 @@ +#%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