Cluster

README.md

@@ -1,4 +1,4 @@
 islandviewer-ui
 ===============
 
-Web UI for Islandviewer
+Web UI for Islandviewer.

scripts/mauve-wrapper.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+#PBS -S /bin/bash
+
+/progressiveMauve --output=$1.xmfa --backbone-output=$2.backbone $3 $4

scripts/mauvewrap.py

@@ -0,0 +1,85 @@
+import subprocess
+import time
+import shutil
+import os
+import xml.etree.ElementTree as ET
+
+#This can file can be moved to lib after testing
+#These paths can be moved to the settings file after testing
+MAUVE_PATH = "/data/Modules/iv-backend/islandviewer_dev/utils/mauve_2.4.0/linux-x64/progressiveMauve"
+MAUVE_OUTPUT_PATH = "/data/Modules/iv-backend/islandviewer/pairwise_mauve"
+
+#Parameters = path to 2 genebank files
+#Returns None
+#Creates an output file at path outputfile and backbone file at path backbonefile
+def runMauve(gbk1,gbk2,outputfile=None,outputbackbonefile=None, async=False):
+    if outputfile is None:
+        outputfile = MAUVE_OUTPUT_PATH+"/"+os.path.splitext(os.path.basename(gbk1))[0]+"-"+os.path.splitext(os.path.basename(gbk2))[0]
+    if outputbackbonefile is None:
+        outputbackbonefile = MAUVE_OUTPUT_PATH+"/"+os.path.splitext(os.path.basename(gbk1))[0]+"-"+os.path.splitext(os.path.basename(gbk2))[0]
+
+    gbk1temppath = MAUVE_OUTPUT_PATH+"/"+os.path.basename(gbk1)
+    gbk2temppath = MAUVE_OUTPUT_PATH+"/"+os.path.basename(gbk2)
+
+    shutil.copyfile(gbk1,gbk1temppath)
+    shutil.copyfile(gbk2,gbk2temppath)
+
+    jobFile = outputfile+".pbs"
+    pbsFile = open(jobFile,"w+")
+    pbsFile.write("#!/bin/bash")
+    pbsFile.write("#PBS -S /bin/bash")
+    pbsFile.write(MAUVE_PATH+" --output="+outputfile+".xmfa --backbone-output="
+                  +outputbackbonefile+".backbone "+gbk1temppath+" "+gbk2temppath)
+    pbsFile.close()
+    sp = subprocess.Popen(["qsub", jobFile], cwd=MAUVE_PATH)
+
+    # waits for job when using torque if async = False
+    if not async:
+        completeFlag = False
+        while not completeFlag:
+            qstatOutput = subprocess.Popen(["qstat", "-x"],stdout=subprocess.PIPE, cwd=MAUVE_PATH)
+            output = qstatOutput.communicate()[0]
+            tree = ET.fromstring(output)
+            matchfile = os.path.basename(jobFile)
+            for index in range(0,len(tree)):
+                currentFile = tree[index][1].text
+                if currentFile == matchfile:
+                    status = tree[index][4].text
+                    if status == 'C':
+                        completeFlag = True
+                    else:
+                        if status != 'R':
+                            completeFlag = True
+                            print "Error has occured to submitted job (cluster)"
+            if not completeFlag:
+                time.sleep(60)
+
+#Given the paths of 2 genebank files, returns path of backbone file if it exists or None if it doesnt
+def retrieveBackboneFile(gbk1,gbk2):
+    backbonepath = MAUVE_OUTPUT_PATH+"/"+os.path.splitext(os.path.basename(gbk1))[0]+"-"+os.path.splitext(os.path.basename(gbk2))[0]+".backbone"
+    if os.path.isfile(backbonepath):
+        return backbonepath
+    else:
+        return None
+
+#Wrapper for retrieving a backbone file. If it doesnt exist, this will call runMauve to create it.
+def getMauveResults(gbk1,gbk2):
+    if retrieveBackboneFile(gbk1,gbk2) is None:
+        runMauve(gbk1,gbk2)
+    return retrieveBackboneFile(gbk1,gbk2)
+
+
+##################### TESTS
+
+def testRunMauve():
+    runMauve("/vagrant/islandviewer-ui/scripts/testFiles/AE009952.gbk","/vagrant/islandviewer-ui/scripts/testFiles/BX936398.gbk")
+
+def testRetrieveBackboneFiles():
+    print(retrieveBackboneFile("/vagrant/islandviewer-ui/scripts/testFiles/AE009952.gbk","/vagrant/islandviewer-ui/scripts/testFiles/BX936398.gbk"))
+
+def testList():
+    #testRunMauve()
+    #testRetrieveBackboneFiles()
+    print getMauveResults("/vagrant/islandviewer-ui/scripts/testFiles/AE009952.gbk","/vagrant/islandviewer-ui/scripts/testFiles/BX936398.gbk")
+
+#testList()

static/css/islandviewer.css

@@ -93,6 +93,10 @@ body {
 	padding: 10px;
 }
 
+input#gene_search_input{
+    width:100%;
+}
+
 .chkLabel input { float: left; margin-top:0.5em;}
 .chkLabel span { display: block; margin-left: 1.5em;}
 
@@ -209,6 +213,9 @@ div.outline {
 	color: #1F1A80;
 	letter-spacing:0.1em;
 	line-height:26px;
+    display: inline-block;
+    white-space: normal;
+    width: 500px;
 }
 
 .linearLabel {
@@ -347,6 +354,10 @@ input[type=file] {
     border: 1px solid #808080;
 }
 
+#outer_circular{
+    white-space: nowrap;
+}
+
 /* Section for GI tables */
 .gitable_fullwidth {
   max-width: 100%;
@@ -636,4 +647,9 @@ input[type=file] {
     transform: rotate(360deg);
   }
 }
+
+.linearchart {
+    width: 100%;
+}
+
 /* END Spinner for loading ranking page*/