--- a/conversion/gbk2rdf/tool_dependencies.xml	Wed Feb 25 08:16:43 2015 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="biopython" version="1.61">
-        <repository changeset_revision="ae9dda584395" name="package_biopython_1_61" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>

--- a/genetic_elements/aragorn/aragorn.py	Wed Feb 25 08:16:43 2015 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,126 +0,0 @@
-
-def delete_galaxy():
-	import sys
-	for index, path in enumerate(sys.path):
-		if "galaxy-dist/" in path:
-			sys.path[index] = ''
-
-#Some modules that are required by RDFLIB are also in galaxy, this messes up the RDF import function. This is not an elegant solution but it works for now.
-delete_galaxy()
-
-from rdflib import Graph, URIRef, Literal,Namespace, XSD, BNode,RDF,RDFS,OWL, ConjunctiveGraph, plugin
-
-# Import RDFLib's default Graph implementation.
-from rdflib.graph import Graph
-
-import sys, os
-
-import rdflib
-import subprocess
-import hashlib
-global URI
-global SubClassOfDict
-SubClassOfDict = {}
-
-URI = "http://csb.wur.nl/genome/"
-global seeAlso
-seeAlso = "rdfs:seeAlso"
-global coreURI
-coreURI = Namespace(URI)
-
-def createClass(uri):
-	#genomeGraph.add((uri,RDF.type,OWL.Class))
-	#genomeGraph.add((uri,RDFS.subClassOf,OWL.Thing))
-	#genomeGraph.add((coreURI["Feature"],RDFS.subClassOf,OWL.Thing))
-	#genomeGraph.add((coreURI["Rna"],RDFS.subClassOf,coreURI["Feature"]))
-	#genomeGraph.add((uri,RDFS.subClassOf,coreURI["Rna"]))
-	return uri
-
-def tmp():
-	import time
-	global tmpFolder
-	tmpFolder = "/tmp/"+str(time.time())+"/"
-	os.mkdir(tmpFolder)
-
-def query():
-	global genomeGraph
-	genomeGraph = Graph()
-	filename = sys.argv[1]
-	genomeGraph.parse(filename, format="turtle")
-	qres = genomeGraph.query('select ?class ?sequence where {?class a ssb:DnaObject . ?class ssb:sequence ?sequence .}')
-	sequences = []
-	for row in qres:
-		print ("Header:",row[0])
-		sequences += [[">"+str(row[0]),str(row[1].strip())]] #.replace("/","-").replace("","")
-
-	return sequences
-
-def aragorn(sequences):
-	for sequence in sequences:
-		#Call aragorn for each contig, for ease of parsing
-		open(tmpFolder+"tmp.seq","w").write('\n'.join(sequence))
-		folder = os.path.realpath(__file__).rsplit("/",2)[0]+"/"
-		cmd = folder+"/tools/aragorn1.2.36/aragorn -fasta "+tmpFolder+"tmp.seq "+' '.join(sys.argv[3:-2])+" > "+tmpFolder+"aragorn.output"
-		print (cmd)
-		os.system(cmd)
-		aragorn = open(tmpFolder+"aragorn.output").readlines()
-# 		string = ''.join(aragorn)
-
-		contig = sequence[0].strip(">").replace("http://csb.wur.nl/genome/","")
-		dnaobjectURI = coreURI[contig]
-		#print (contig)
-		for line in aragorn:
-			if ">" in line:
-				print (line.split())
-				try:
-					trna, pos = line.split()[1:]
-				except:
-					try:
-						trna, pos = line.split()
-					except:
-						if "(Permuted)" in line:
-							trna, permute, pos = line.split()[1:]
-							
-				if "tRNA-" in line:
-					trna, codon = (trna.strip(">)").split("(",1))
-				else:
-					trna = trna.strip(">").strip() #Actually a tmRNA...
-					codon = ''
-				trnaClass = createClass(coreURI[trna.split("-")[0].title()]) #trna or tmrna
-				SubClassOfDict[trna.split("-")[0].title()] = 1
-				if "c" in pos[0]: #complementary
-					stop, start = pos.split("[")[1].split("]")[0].split(",")
-				else:
-					start, stop = pos.split("[")[1].split("]")[0].split(",")
-				trnaURI = coreURI[contig+"/trna-aragorn_1_2_36-"+trna.lower() +"/"+ start +"_"+ stop]
-				genomeGraph.add((dnaobjectURI, coreURI["feature"] , trnaURI))
-				genomeGraph.add((trnaURI, RDF.type,trnaClass))
-				genomeGraph.add((trnaURI, coreURI["begin"] , Literal(start,datatype=XSD.integer)))
-				genomeGraph.add((trnaURI, coreURI["end"] , Literal(stop,datatype=XSD.integer)))
-				genomeGraph.add((trnaURI, coreURI["trna_type"] , Literal(trna)))
-				genomeGraph.add((trnaURI, coreURI["trna_anti"] , Literal(codon)))
-				genomeGraph.add((trnaURI, coreURI["tool"] , Literal("aragorn")))
-				genomeGraph.add((trnaURI, coreURI["version"] , Literal("1.2.36")))
-				genomeGraph.add((trnaURI, coreURI["sourcedb"], Literal(sys.argv[sys.argv.index("-sourcedb")+1])))
-
-def subClassOfBuilder():
-	for subclass in SubClassOfDict:
-		genomeGraph.add((coreURI["Feature"],RDFS.subClassOf,OWL.Thing))
-		genomeGraph.add((coreURI["Rna"],RDFS.subClassOf,coreURI["Feature"]))
-		genomeGraph.add((coreURI[subclass],RDFS.subClassOf,coreURI["Rna"]))
-		genomeGraph.add((coreURI["Rna"], RDF.type,OWL.Class))
-
-def save():
-	#Create the subclass off instances
-	#subClassOfBuilder()
-	## Saves the file
-	data = genomeGraph.serialize(format='turtle')
-	open(sys.argv[2],"wb").write(data)
-
-def main():
-	tmp()
-	sequences = query()
-	aragorn(sequences)
-	save()
-
-main()

--- a/genetic_elements/aragorn/tool_dependencies.xml	Wed Feb 25 08:16:43 2015 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="aragorn" version="1.2.36">
-        <repository changeset_revision="f09e2902e6ed" name="package_aragorn_1_2_36" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <set_environment version="1.0">
-        <environment_variable action="set_to" name="TRNAPRED_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
-</tool_dependency>