Add all the source codes into the github.

16 files changed, 892 insertions, 0 deletions

diff --git a/web/webqtl/cmdLine/__init__.py b/web/webqtl/cmdLine/__init__.py
new file mode 100755
index 00000000..e69de29b
--- /dev/null
+++ b/web/webqtl/cmdLine/__init__.py
diff --git a/web/webqtl/cmdLine/cmdCompCorrPage.py b/web/webqtl/cmdLine/cmdCompCorrPage.py
new file mode 100755
index 00000000..f53e1bce
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdCompCorrPage.py
@@ -0,0 +1,49 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+import os
+
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility import webqtlUtil
+
+
+
+class cmdCompCorrPage(templatePage):
+
+	def __init__(self,fd):
+
+		templatePage.__init__(self, fd)
+
+		filename = self.session("Correlation Comparison", "Correlation Comparison in progress")
+
+		webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session'))
+
+		url = webqtlConfig.REFRESHDIR  %  (webqtlConfig.CGIDIR, self.filename)
+
+		os.system("%s %swebqtlCmdLine.py correlationComparison %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename))
+
+		self.redirection = url
diff --git a/web/webqtl/cmdLine/cmdCorrelationPage.py b/web/webqtl/cmdLine/cmdCorrelationPage.py
new file mode 100755
index 00000000..4c76dc0b
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdCorrelationPage.py
@@ -0,0 +1,53 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+import os
+
+
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility import webqtlUtil
+
+
+#########################################
+#      Correlation Page
+#########################################
+class cmdCorrelationPage(templatePage):
+
+	def __init__(self,fd):
+
+		templatePage.__init__(self, fd)
+
+		filename = self.session("Correlation", "Correlation Computation in Progress")
+
+		webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session'))
+
+		url = webqtlConfig.REFRESHDIR  %  (webqtlConfig.CGIDIR, self.filename)
+
+		os.system("%s %swebqtlCmdLine.py correlation %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename))
+
+		self.redirection = url
+
diff --git a/web/webqtl/cmdLine/cmdDirectPlotPage.py b/web/webqtl/cmdLine/cmdDirectPlotPage.py
new file mode 100755
index 00000000..21e936dc
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdDirectPlotPage.py
@@ -0,0 +1,49 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+import os
+
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility import webqtlUtil
+
+
+
+class cmdDirectPlotPage(templatePage):
+
+	def __init__(self,fd):
+
+		templatePage.__init__(self, fd)
+
+		filename = self.session("Pair Scan", "Pair Scan Computation in Progress")
+
+		webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session'))
+
+		url = webqtlConfig.REFRESHDIR  %  (webqtlConfig.CGIDIR, self.filename)
+
+		os.system("%s %swebqtlCmdLine.py directplot %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename))
+
+		self.redirection = url
diff --git a/web/webqtl/cmdLine/cmdHeatmapPage.py b/web/webqtl/cmdLine/cmdHeatmapPage.py
new file mode 100755
index 00000000..e96f3449
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdHeatmapPage.py
@@ -0,0 +1,52 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+import os
+
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility import webqtlUtil
+
+	
+#########################################
+#      QTL Heatmap Page
+#########################################
+
+class cmdHeatmapPage(templatePage):
+
+	def __init__(self,fd):
+
+		templatePage.__init__(self, fd)
+
+		filename = self.session("QTL Heatmap", "Computing QTL Heatmap")
+
+		webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session'))
+
+		url = webqtlConfig.REFRESHDIR  %  (webqtlConfig.CGIDIR, self.filename)
+
+		os.system("%s %swebqtlCmdLine.py heatmap %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename))
+
+		self.redirection = url
diff --git a/web/webqtl/cmdLine/cmdIntervalMappingPage.py b/web/webqtl/cmdLine/cmdIntervalMappingPage.py
new file mode 100755
index 00000000..8e0a3d92
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdIntervalMappingPage.py
@@ -0,0 +1,75 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+import os
+
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility import webqtlUtil
+
+#########################################
+#      Interval Mapping Page
+#########################################
+
+class cmdIntervalMappingPage(templatePage):
+
+	def __init__(self,fd):
+
+		templatePage.__init__(self, fd)
+
+		wtext = "Mapping "
+		try:
+			selectedChr = int(fd.formdata.getvalue('chromosomes')) + 1
+			if selectedChr < 1:
+				raise "ValueError"
+			if selectedChr == 21 or (selectedChr == 20 and fd.RISet != 'HXBBXH'):
+				selectedChr = 'X'
+			wtext += 'chromosome %s ' % selectedChr
+		except:
+			wtext += 'whole genome '
+
+		perm = 0
+		if fd.formdata.getvalue('permCheck'):
+			perm = 1
+			wtext += 'with %d permutation tests ' % fd.nperm
+
+		boot = 0
+		if fd.formdata.getvalue('bootCheck'):
+			boot = 1
+			if perm:
+				wtext += 'and %d bootstrap tests ' % fd.nboot
+			else:
+				wtext += 'with %d bootstrap tests ' % fd.nboot
+		
+		if boot == 0 and perm == 0:
+			wtext +=  "without permutation or bootstrap tests"
+		
+		filename = self.session("Interval Mapping", wtext)
+		webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session'))
+		url = webqtlConfig.REFRESHDIR  %  (webqtlConfig.CGIDIR, self.filename)
+		os.system("%s %swebqtlCmdLine.py interval %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename))
+		self.redirection = url
+
diff --git a/web/webqtl/cmdLine/cmdMarkerRegressionPage.py b/web/webqtl/cmdLine/cmdMarkerRegressionPage.py
new file mode 100755
index 00000000..fb974e33
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdMarkerRegressionPage.py
@@ -0,0 +1,47 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by NL 2011/03/15
+#
+# Last updated by NL 2011/03/15
+
+import os
+
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility import webqtlUtil
+
+	
+#########################################
+#      Marker RegressionPage Page
+#########################################
+
+class cmdMarkerRegressionPage(templatePage):
+
+	def __init__(self,fd):
+		templatePage.__init__(self, fd)
+
+		filename = self.session("Genome Association Result", "Computing Genome Association Results")
+		webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session'))
+		url = webqtlConfig.REFRESHDIR  %  (webqtlConfig.CGIDIR, self.filename)
+		os.system("%s %swebqtlCmdLine.py markerRegression %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename))
+		self.redirection = url
diff --git a/web/webqtl/cmdLine/cmdNetworkGraphPage.py b/web/webqtl/cmdLine/cmdNetworkGraphPage.py
new file mode 100755
index 00000000..a16fcbaf
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdNetworkGraphPage.py
@@ -0,0 +1,49 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+import os
+
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility import webqtlUtil
+
+		
+
+class cmdNetworkGraphPage(templatePage):
+
+	def __init__(self, fd):
+
+		templatePage.__init__(self, fd)
+
+		filename = self.session("Network Graph", "Computing Network Graph")
+
+		webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename + '.session'))
+
+		url = webqtlConfig.REFRESHDIR % (webqtlConfig.CGIDIR, self.filename)
+
+		os.system("%s %swebqtlCmdLine.py networkGraph %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename))
+
+		self.redirection = url
diff --git a/web/webqtl/cmdLine/cmdPartialCorrelationPage.py b/web/webqtl/cmdLine/cmdPartialCorrelationPage.py
new file mode 100755
index 00000000..fb5324c6
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdPartialCorrelationPage.py
@@ -0,0 +1,50 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+import os
+
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility import webqtlUtil
+
+########################################
+#       Partial Correlation Page
+########################################
+class cmdPartialCorrelationPage(templatePage):
+
+        def __init__(self,fd):
+
+                templatePage.__init__(self, fd)
+
+                filename = self.session("Partial Correlation", "Partial Correlation in Progress")
+
+                webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session'))
+
+                url = webqtlConfig.REFRESHDIR  %  (webqtlConfig.CGIDIR, self.filename)
+
+                os.system("%s %swebqtlCmdLine.py partialCorrelation %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename))
+
+                self.redirection = url
diff --git a/web/webqtl/cmdLine/cmdQTLminerPage.py b/web/webqtl/cmdLine/cmdQTLminerPage.py
new file mode 100755
index 00000000..2197d3ce
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdQTLminerPage.py
@@ -0,0 +1,47 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by NL 2011/03/15
+#
+# Last updated by NL 2011/03/15
+
+import os
+
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility import webqtlUtil
+
+	
+#########################################
+#      QTLminer Page
+#########################################
+
+class cmdQTLminerPage(templatePage):
+
+	def __init__(self,fd):
+		templatePage.__init__(self, fd)
+
+		filename = self.session("QTLminer Result", "Computing QTLminer Results")
+		webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session'))
+		url = webqtlConfig.REFRESHDIR  %  (webqtlConfig.CGIDIR, self.filename)
+		os.system("%s %swebqtlCmdLine.py QTLminer %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename))
+		self.redirection = url
diff --git a/web/webqtl/cmdLine/cmdShowAllPage.py b/web/webqtl/cmdLine/cmdShowAllPage.py
new file mode 100755
index 00000000..37e159e9
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdShowAllPage.py
@@ -0,0 +1,50 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+import os
+
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility import webqtlUtil
+
+
+
+class cmdShowAllPage(templatePage):
+
+	def __init__(self,fd):
+
+		templatePage.__init__(self, fd)
+
+		filename = self.session("Generate Report", "Generating Report. Please be Patient")
+
+		webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session'))
+
+		url = webqtlConfig.REFRESHDIR  %  (webqtlConfig.CGIDIR, self.filename)
+
+		os.system("%s %swebqtlCmdLine.py genreport %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename))
+
+		self.redirection = url
+
diff --git a/web/webqtl/cmdLine/cmdShowAllPage2.py b/web/webqtl/cmdLine/cmdShowAllPage2.py
new file mode 100755
index 00000000..a1ac172f
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdShowAllPage2.py
@@ -0,0 +1,55 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+import os
+
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility import webqtlUtil
+
+
+
+#########################################
+#      Generate Report Page
+#########################################
+
+class cmdShowAllPage2(templatePage):
+
+	def __init__(self,fd):
+
+		templatePage.__init__(self, fd)
+
+		filename = self.session("Generate Report v2", "Generating Report v2. Please be Patient")
+
+		webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session'))
+
+		url = webqtlConfig.REFRESHDIR  %  (webqtlConfig.CGIDIR, self.filename)
+
+		os.system("%s %swebqtlCmdLine.py genreport2 %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename))
+
+		self.redirection = url
+
+
diff --git a/web/webqtl/cmdLine/cmdSnpBrowserResultPage.py b/web/webqtl/cmdLine/cmdSnpBrowserResultPage.py
new file mode 100755
index 00000000..54cb1181
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdSnpBrowserResultPage.py
@@ -0,0 +1,47 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by NL 2011/03/15
+#
+# Last updated by NL 2011/03/15
+
+import os
+
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility import webqtlUtil
+
+	
+#########################################
+#      SnpBrowser Page
+#########################################
+
+class cmdSnpBrowserResultPage(templatePage):
+
+	def __init__(self,fd):
+		templatePage.__init__(self, fd)
+
+		filename = self.session("Variant Browser Result", "Computing Variant Browser Results")
+		webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session'))
+		url = webqtlConfig.REFRESHDIR  %  (webqtlConfig.CGIDIR, self.filename)
+		os.system("%s %swebqtlCmdLine.py snpbrowser %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename))
+		self.redirection = url
diff --git a/web/webqtl/cmdLine/cmdTissueCorrelationResultPage.py b/web/webqtl/cmdLine/cmdTissueCorrelationResultPage.py
new file mode 100755
index 00000000..1f28953c
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdTissueCorrelationResultPage.py
@@ -0,0 +1,47 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by NL 2011/03/15
+#
+# Last updated by NL 2011/03/15
+
+import os
+
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility import webqtlUtil
+
+	
+#########################################
+#      SnpBrowser Page
+#########################################
+
+class cmdTissueCorrelationResultPage(templatePage):
+
+	def __init__(self,fd):
+		templatePage.__init__(self, fd)
+
+		filename = self.session("Tissue Correlation Result Page", "Computing Tissue Correlation Result")
+		webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session'))
+		url = webqtlConfig.REFRESHDIR  %  (webqtlConfig.CGIDIR, self.filename)
+		os.system("%s %swebqtlCmdLine.py tissueCorrelation %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename))
+		self.redirection = url
diff --git a/web/webqtl/cmdLine/procPage.py b/web/webqtl/cmdLine/procPage.py
new file mode 100755
index 00000000..03ce242c
--- /dev/null
+++ b/web/webqtl/cmdLine/procPage.py
@@ -0,0 +1,46 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+#--Only imported by WebQTL.py -KA
+
+#Xiaodong changed the dependancy structure
+
+import os
+
+from base import webqtlConfig
+
+
+class procPage:
+	def __init__(self, myID, req):
+		try:
+			fp = open(os.path.join(webqtlConfig.TMPDIR, myID + '.html'), 'rb')
+		except:
+			fp = open(os.path.join(webqtlConfig.ChangableHtmlPath, 'missing.html'), 'rb')
+		
+		content = fp.read()
+		fp.close()
+		req.write(content)
+			
diff --git a/web/webqtl/cmdLine/webqtlCmdLine.py b/web/webqtl/cmdLine/webqtlCmdLine.py
new file mode 100755
index 00000000..ebc10e1c
--- /dev/null
+++ b/web/webqtl/cmdLine/webqtlCmdLine.py
@@ -0,0 +1,176 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+
+
+########################################################
+#XZ, Aug 10, 2010
+#This part is the temporary solution to make python be able to find other subpackages.
+#We can't set global environment because there are many branches on the development machine.
+
+import sys, os
+
+current_file_name = __file__
+pathname = os.path.dirname( current_file_name )
+abs_path = os.path.abspath(pathname)
+sys.path.insert(0, abs_path + '/..')
+
+########################################################
+
+
+
+import traceback
+import string
+import cPickle
+
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility import webqtlUtil
+
+
+if __name__ == "__main__":
+	try:
+		if len(sys.argv) > 2:
+			getID = string.lower(sys.argv[1])
+		else:
+			raise ValueError
+	
+		cmdtype = sys.argv[1]
+		sessionfile =  sys.argv[2]
+
+		fd = None
+		
+		fp = open(os.path.join(webqtlConfig.TMPDIR, sessionfile + '.session'), 'rb')
+		fd = cPickle.load(fp)
+		fp.close()
+
+		if cmdtype == "heatmap":
+			from heatmap import heatmapPage
+			reload(heatmapPage)
+			page = heatmapPage.heatmapPage(fd)
+			page.writeFile(sessionfile+'.html')
+		elif cmdtype == "directplot":
+			from pairScan import DirectPlotPage
+			reload(DirectPlotPage)
+			page = DirectPlotPage.DirectPlotPage(fd)
+			page.writeFile(sessionfile+'.html')
+		elif cmdtype == "networkGraph":
+			from networkGraph import networkGraphPage
+			reload(networkGraphPage)
+			page = networkGraphPage.networkGraphPage(fd)
+			page.writeFile(sessionfile+'.html')
+		elif cmdtype == "interval":
+			from intervalMapping import IntervalMappingPage
+			reload(IntervalMappingPage)
+			page = IntervalMappingPage.IntervalMappingPage(fd)
+			page.writeFile(sessionfile+'.html')
+		elif cmdtype == "correlation":
+			from correlation import CorrelationPage
+			reload (CorrelationPage)
+			page = CorrelationPage.CorrelationPage(fd)
+			page.writeFile(sessionfile+'.html')
+                elif cmdtype == "partialCorrelation":
+                        from correlation import PartialCorrDBPage
+			reload(PartialCorrDBPage)
+                        page = PartialCorrDBPage.PartialCorrDBPage(fd)
+                        page.writeFile(sessionfile+'.html')
+		elif cmdtype == "correlationComparison":
+			from compareCorrelates import multitrait
+			reload(multitrait)
+			page = multitrait.compCorrPage(fd)
+			page.writeFile(sessionfile+'.html')
+		elif cmdtype == "genreport": # Generate Report Page
+			spacer = '</TR></Table><Table width=900 cellSpacing=0 cellPadding=5><TR>'
+
+			from basicStatistics import BasicStatisticsPage
+			reload(BasicStatisticsPage)
+			page1 = BasicStatisticsPage.BasicStatisticsPage(fd)
+
+			if not fd.formdata.getvalue('bsCheck'):
+				page1.dict['body'] = ""
+
+			if fd.formdata.getvalue('tcCheck'):
+				from correlation import CorrelationPage
+				reload(CorrelationPage)
+				page2 = CorrelationPage.CorrelationPage(fd)
+				page1.dict['body'] += spacer + str(page2.dict['body'])
+				page1.dict['js1'] +=  page2.dict['js1']
+
+			if fd.formdata.getvalue('imCheck'):
+				from intervalMapping import IntervalMappingPage
+				reload(IntervalMappingPage)
+				page3 = IntervalMappingPage.IntervalMappingPage(fd)
+				page1.dict['body'] += spacer + str(page3.dict['body'])
+
+			if fd.formdata.getvalue('mrCheck'):
+				from markerRegression import MarkerRegressionPage
+				reload(MarkerRegressionPage)
+				page4 = MarkerRegressionPage.MarkerRegressionPage(fd)
+				page1.dict['body'] += spacer + str(page4.dict['body'])
+
+			if fd.formdata.getvalue('psCheck'):
+				from pairScan import DirectPlotPage
+				reload(DirectPlotPage)
+				page5 = DirectPlotPage.DirectPlotPage(fd)
+				page1.dict['body'] += spacer + str(page5.dict['body'])
+									 
+			page1.writeFile(sessionfile+'.html')
+			
+		elif cmdtype == "genreport2": # Generate Report Page v2
+			spacer = '</TR></Table><Table width=900 cellSpacing=0 cellPadding=5><TR>'
+
+			from basicStatistics import BasicStatisticsPage_alpha
+			reload(BasicStatisticsPage_alpha)
+			page1 = BasicStatisticsPage_alpha.BasicStatisticsPage_alpha(fd)
+			page1.writeFile(sessionfile+'.html')
+		elif cmdtype == "snpbrowser":
+			from snpBrowser import snpBrowserPage
+			reload(snpBrowserPage)
+			page = snpBrowserPage.snpBrowserPage(fd)
+			page.writeFile(sessionfile+'.html')
+		elif cmdtype == "QTLminer":
+			from qtlminer import QTLminer
+			reload(QTLminer)
+			page = QTLminer.QTLminer(fd)
+			page.writeFile(sessionfile+'.html')
+		elif cmdtype == "tissueCorrelation":
+			from correlationMatrix import TissueCorrelationPage
+			reload(TissueCorrelationPage)
+			page = TissueCorrelationPage.TissueCorrelationPage(fd)
+			page.writeFile(sessionfile+'.html')	
+		elif cmdtype == "markerRegression":
+			from markerRegression import MarkerRegressionPage
+			reload(MarkerRegressionPage)
+			page = MarkerRegressionPage.MarkerRegressionPage(fd)
+			page.writeFile(sessionfile+'.html')				
+		else:
+			raise ValueError
+	except:
+		fp = open(os.path.join(webqtlConfig.TMPDIR, sessionfile +'.html'), 'wb')
+		fp.write('\n\n<pre>')
+		traceback.print_exc(file=fp)							
+		fp.write('\n</pre>')
+		fp.close()