adding samtools/htslib/tabix/bcftools 1.10

envfiles/bcftools/1.10

+#%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

envfiles/htslib/1.10.2

+#%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

envfiles/samtools/1.10

+#%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

envfiles/tabix/0.2.6

+#%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

envfiles/tabix/1.10.2

+#%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

envfiles/tabix/1.2.1

+#%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