mostly working new summary and dynamic Krona install

marbl · Oct 19, 2012 · 3ba5173 · 3ba5173
1 parent b8b4e7f
commit 3ba5173
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Showing 22 changed files with 635 additions and 9,623 deletions.
diff --git a/INSTALL.py b/INSTALL.py
@@ -30,6 +30,7 @@
 OSTYPE="Linux"
 OSVERSION="1"
 MACHINETYPE="x86_64"
+kronaTools = "KronaTools-2.2"
 
 #identify machine type
 p = subprocess.Popen("echo `uname`", shell=True, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
@@ -230,6 +231,29 @@
          os.system("cd wgs-7.0/src && gmake")
       os.system("mv wgs-7.0 CA")
 
+if not os.path.exists("KronaTools") or 0:
+    print "KronaTools not found, needed for Postprocess, download now?"
+    if silentInstall:
+       dl = 'y'
+    else:
+       dl = raw_input("Enter Y/N: ")
+    if dl == 'y' or dl == 'Y':
+        # TODO: KronaTools should be on the FTP site for robustness to URL changes
+        os.system("wget http://downloads.sourceforge.net/project/krona/KronaTools%20%28Mac%2C%20Linux%29/" + kronaTools + ".tar?r=&ts=1350316432&use_mirror=superb-dca3")
+        os.system("tar -xvf %s.tar"%(kronaTools))
+        os.system("rm -rf %s.tar"%(kronaTools))
+        os.system("cd %s && ./install.pl --prefix=."%(kronaTools))
+        os.system("mv %s KronaTools"%(kronaTools))
+
+if not os.path.exists("KronaTools/taxonomy/taxonomy.tab") or 0:
+    print "KronaTools taxonomy data not found, needed for Postprocess, download now (will take around 20 minutes)?"
+    if silentInstall:
+       dl = 'y'
+    else:
+       dl = raw_input("Enter Y/N: ")
+    if dl == 'y' or dl == 'Y':
+        os.system("cd KronaTools && ./updateTaxonomy.sh")
+
 # make sure we have setuptools available
 sys.path.append(sys.path[0] + os.sep + "Utilities" + os.sep + "python")
 from get_setuptools import use_setuptools

diff --git a/Utilities/javascript/Assemble.html b/Utilities/javascript/Assemble.html
@@ -0,0 +1,19 @@
+<head>
+<style>
+
+#bigPicture
+{
+	width:100%;
+	height:100%;
+	background:url(ContigSizes.png);
+	background-size:contain;
+	background-repeat:no-repeat;
+	background-position:center;
+}
+</style>
+</head>
+
+<body style="margin:0px">
+	<div id="bigPicture">
+	</div>
+</body>
diff --git a/Utilities/javascript/FindORFs.html b/Utilities/javascript/FindORFs.html
@@ -0,0 +1,19 @@
+<head>
+<style>
+
+#bigPicture
+{
+	width:100%;
+	height:100%;
+	background:url(ORFSizes.png);
+	background-size:contain;
+	background-repeat:no-repeat;
+	background-position:center;
+}
+</style>
+</head>
+
+<body style="margin:0px">
+	<div id="bigPicture">
+	</div>
+</body>
diff --git a/Utilities/javascript/FindScaffoldORFs.html b/Utilities/javascript/FindScaffoldORFs.html
@@ -0,0 +1,19 @@
+<head>
+<style>
+
+#bigPicture
+{
+	width:100%;
+	height:100%;
+	background:url(SCFORFSizes.png);
+	background-size:contain;
+	background-repeat:no-repeat;
+	background-position:center;
+}
+</style>
+</head>
+
+<body style="margin:0px">
+	<div id="bigPicture">
+	</div>
+</body>
diff --git a/Utilities/javascript/Scaffold.html b/Utilities/javascript/Scaffold.html
@@ -0,0 +1,19 @@
+<head>
+<style>
+
+#bigPicture
+{
+	width:100%;
+	height:100%;
+	background:url(ScaffoldSizes.png);
+	background-size:contain;
+	background-repeat:no-repeat;
+	background-position:center;
+}
+</style>
+</head>
+
+<body style="margin:0px">
+	<div id="bigPicture">
+	</div>
+</body>
diff --git a/Utilities/javascript/abundance.js b/Utilities/javascript/abundance.js
diff --git a/Utilities/javascript/annotate.js b/Utilities/javascript/annotate.js
diff --git a/Utilities/javascript/assemble.js b/Utilities/javascript/assemble.js
diff --git a/Utilities/javascript/findorfs.js b/Utilities/javascript/findorfs.js
diff --git a/Utilities/javascript/findscaffoldorfs.js b/Utilities/javascript/findscaffoldorfs.js