Version bumps

README.md

@@ -18,7 +18,7 @@ Once the download has been completed, unpack the downloaded archive.
 The following command will automatically download and unpack the archive in the newly created `rabix` directory:
 
 ```sh
-wget https://github.com/rabix/bunny/releases/download/v1.0.4-5/rabix-1.0.4.tar.gz -O rabix-1.0.4.tar.gz && tar -xvf rabix-1.0.4.tar.gz
+wget https://github.com/rabix/bunny/releases/download/v1.0.5/rabix-1.0.5.tar.gz -O rabix-1.0.5.tar.gz && tar -xvf rabix-1.0.5.tar.gz
 ```
 
 

pom.xml

@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>org.rabix</groupId>
 	<artifactId>rabix</artifactId>
-	<version>1.0.4</version>
+	<version>1.0.5</version>
 	<packaging>pom</packaging>
 	<name>Rabix Executor</name>
 	<description>

rabix-backend-api/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.rabix</groupId>
 		<artifactId>rabix</artifactId>
-		<version>1.0.4</version>
+		<version>1.0.5</version>
 	</parent>
 	<artifactId>rabix-backend-api</artifactId>
 	<name>rabix-backend-api</name>

rabix-backend-lsf/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.rabix</groupId>
 		<artifactId>rabix</artifactId>
-		<version>1.0.4</version>
+		<version>1.0.5</version>
 	</parent>
 	<artifactId>rabix-backend-lsf</artifactId>
 	<name>rabix-backend-lsf</name>

rabix-backend-tes/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.rabix</groupId>
 		<artifactId>rabix</artifactId>
-		<version>1.0.4</version>
+		<version>1.0.5</version>
 	</parent>
 	<artifactId>rabix-backend-tes</artifactId>
 	<name>rabix-backend-tes</name>

rabix-bindings-cwl/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.rabix</groupId>
 		<artifactId>rabix</artifactId>
-		<version>1.0.4</version>
+		<version>1.0.5</version>
 	</parent>
 	<artifactId>rabix-bindings-cwl</artifactId>
 	<name>rabix-bindings-cwl</name>

rabix-bindings-draft2/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.rabix</groupId>
 		<artifactId>rabix</artifactId>
-		<version>1.0.4</version>
+		<version>1.0.5</version>
 	</parent>
 	<artifactId>rabix-bindings-draft2</artifactId>
 	<name>rabix-bindings-draft2</name>

rabix-bindings-draft3/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.rabix</groupId>
 		<artifactId>rabix</artifactId>
-		<version>1.0.4</version>
+		<version>1.0.5</version>
 	</parent>
 	<artifactId>rabix-bindings-draft3</artifactId>
 	<name>rabix-bindings-draft3</name>

rabix-bindings-sb/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.rabix</groupId>
 		<artifactId>rabix</artifactId>
-		<version>1.0.4</version>
+		<version>1.0.5</version>
 	</parent>
 	<artifactId>rabix-bindings-sb</artifactId>
 	<name>rabix-bindings-sb</name>

rabix-bindings/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.rabix</groupId>
 		<artifactId>rabix</artifactId>
-		<version>1.0.4</version>
+		<version>1.0.5</version>
 	</parent>
 	<artifactId>rabix-bindings</artifactId>
 	<name>rabix-bindings</name>

rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/.Transcribe.meta/job.json

@@ -0,0 +1,54 @@
+{
+  "id" : "50539b1b-292f-3e24-9e85-0970389a5f8a",
+  "parentId" : "3b13e065-ef67-4f49-9da6-5196c50412cb",
+  "rootId" : "3b13e065-ef67-4f49-9da6-5196c50412cb",
+  "name" : "root.Transcribe",
+  "app" : "data:text/plain;base64,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",
+  "status" : "COMPLETED",
+  "inputs" : {
+    "input_file" : [ {
+      "size" : 29,
+      "path" : "/Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/data/input.txt",
+      "location" : "file:///Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/data/input.txt",
+      "name" : "input.txt",
+      "dirname" : "/Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/data",
+      "nameroot" : "input",
+      "nameext" : ".txt",
+      "checksum" : "sha1$06fec0ada27fe482c082e01fad1dc0e1775ef1c3",
+      "secondaryFiles" : [ ],
+      "properties" : {
+        "sbg:metadata" : null
+      },
+      "$type" : "File"
+    } ],
+    "output_filename" : null,
+    "verbose" : true
+  },
+  "outputs" : {
+    "output_file_glob" : {
+      "size" : 29,
+      "path" : "/Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Transcribe/rna.txt",
+      "location" : "file:///Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Transcribe/rna.txt",
+      "name" : "rna.txt",
+      "dirname" : "/Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Transcribe",
+      "nameroot" : "rna",
+      "nameext" : ".txt",
+      "checksum" : "sha1$3e31c660fdbd1b32b188368ee31d29f79ee42400",
+      "secondaryFiles" : [ ],
+      "properties" : {
+        "sbg:metadata" : null
+      },
+      "$type" : "File"
+    }
+  },
+  "resources" : {
+    "cpu" : 8,
+    "memMB" : 12743,
+    "diskSpaceMB" : null,
+    "networkAccess" : false,
+    "workingDir" : "/Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Transcribe",
+    "tmpDir" : "/Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Transcribe",
+    "outDirSize" : null,
+    "tmpDirSize" : null
+  }
+}

rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/.Translate.meta/job.json

@@ -0,0 +1,53 @@
+{
+  "id" : "28554025-11c7-35a7-909c-de7bae2f70c0",
+  "parentId" : "3b13e065-ef67-4f49-9da6-5196c50412cb",
+  "rootId" : "3b13e065-ef67-4f49-9da6-5196c50412cb",
+  "name" : "root.Translate",
+  "app" : "data:text/plain;base64,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",
+  "status" : "COMPLETED",
+  "inputs" : {
+    "input_file" : [ {
+      "size" : 29,
+      "path" : "/Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Transcribe/rna.txt",
+      "location" : "file:///Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Transcribe/rna.txt",
+      "name" : "rna.txt",
+      "dirname" : "/Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Transcribe",
+      "nameroot" : "rna",
+      "nameext" : ".txt",
+      "checksum" : "sha1$3e31c660fdbd1b32b188368ee31d29f79ee42400",
+      "secondaryFiles" : [ ],
+      "properties" : {
+        "sbg:metadata" : null
+      },
+      "$type" : "File"
+    } ],
+    "output_filename" : null
+  },
+  "outputs" : {
+    "output_protein" : {
+      "size" : 9,
+      "path" : "/Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Translate/protein.txt",
+      "location" : "file:///Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Translate/protein.txt",
+      "name" : "protein.txt",
+      "dirname" : "/Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Translate",
+      "nameroot" : "protein",
+      "nameext" : ".txt",
+      "checksum" : "sha1$55adf0ec2ecc6aee57a774d48216ac5a97d6e5ba",
+      "secondaryFiles" : [ ],
+      "properties" : {
+        "sbg:metadata" : null
+      },
+      "$type" : "File"
+    }
+  },
+  "resources" : {
+    "cpu" : 8,
+    "memMB" : 12743,
+    "diskSpaceMB" : null,
+    "networkAccess" : false,
+    "workingDir" : "/Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Translate",
+    "tmpDir" : "/Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Translate",
+    "outDirSize" : null,
+    "tmpDirSize" : null
+  }
+}

rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Transcribe/cmd.log

@@ -0,0 +1 @@
+python transcribe_argparse.py -d /Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/data/input.txt --verbose > /Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Transcribe/rna.txt

rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Transcribe/cwl.output.json

@@ -0,0 +1,13 @@
+{
+  "output_file_glob" : {
+    "basename" : "rna.txt",
+    "checksum" : "sha1$3e31c660fdbd1b32b188368ee31d29f79ee42400",
+    "class" : "File",
+    "dirname" : "/Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Transcribe",
+    "location" : "file:///Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Transcribe/rna.txt",
+    "nameext" : ".txt",
+    "nameroot" : "rna",
+    "path" : "/Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Transcribe/rna.txt",
+    "size" : 29
+  }
+}

rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Transcribe/job.err.log

@@ -0,0 +1,2 @@
+Your original DNA sequence: CTACGATCAGCAGCTACGACTACTAGCA
+Your translated mRNA sequence: GAUGCUAGUCGUCGAUGCUGAUGAUCGU

rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Transcribe/rna.txt

@@ -0,0 +1 @@
+GAUGCUAGUCGUCGAUGCUGAUGAUCGU

rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Transcribe/transcribe_argparse.py

@@ -0,0 +1,33 @@
+#!/usr/bin/env/python
+import argparse
+import re
+import sys
+
+def transcribe(args):
+	# create a transcription map and use regex to translate
+	map = {"A":"U", "T":"A", "C":"G", "G":"C"}
+	map = dict((re.escape(k), v) for k, v in map.iteritems())
+	pattern = re.compile("|".join(map.keys()))
+	DNA = args['dna'].read().strip()
+	mRNA = pattern.sub(lambda m: map[re.escape(m.group(0))], DNA)
+
+	# write a verbose output to stderr and just mRNA to sdtout 
+	if args['verbose']:
+		sys.stderr.write("Your original DNA sequence: " + DNA + "\n")
+		sys.stderr.write("Your translated mRNA sequence: " + mRNA + "\n")
+	sys.stdout.write(mRNA + '\n')
+	sys.exit(0)
+	return mRNA
+
+if __name__ == "__main__":
+	""" Parse the command line arguments """
+	parser = argparse.ArgumentParser()
+	parser.add_argument("-d", "--dna", type=argparse.FileType("r"), default=sys.stdin)
+	parser.add_argument("-v", "--verbose", action="store_true", default=False)
+	# By setting args as var(...), it becomes a dict, so 'dna' is a key
+	# Alternative use: args = parser.parse_args(), and 'dna' is an attr of args!
+	# You must change how you call the args you parse based on this usage! 
+	args = vars(parser.parse_args())
+
+	""" Run the desired methods """
+	transcribe(args)

rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Translate/cmd.log

@@ -0,0 +1 @@
+python translate.py -r /Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Transcribe/rna.txt > /Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Translate/protein.txt

rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Translate/cwl.output.json

@@ -0,0 +1,13 @@
+{
+  "output_protein" : {
+    "basename" : "protein.txt",
+    "checksum" : "sha1$55adf0ec2ecc6aee57a774d48216ac5a97d6e5ba",
+    "class" : "File",
+    "dirname" : "/Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Translate",
+    "location" : "file:///Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Translate/protein.txt",
+    "nameext" : ".txt",
+    "nameroot" : "protein",
+    "path" : "/Users/milosljubinkovic/git/bunny/rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Translate/protein.txt",
+    "size" : 9
+  }
+}

rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Translate/protein.txt

@@ -0,0 +1 @@
+MLVVDADD

rabix-cli/examples/dna2protein/dna2protein.cwl-2018-03-22-135251.500/root/Translate/translate.py

@@ -0,0 +1,41 @@
+#!/usr/bin/env/python
+import argparse
+import sys
+
+def translate(args):
+	mRNA = args['mRNA'].read().strip()
+	codon_map = {"UUU":"F", "UUC":"F", "UUA":"L", "UUG":"L",
+    "UCU":"S", "UCC":"S", "UCA":"S", "UCG":"S",
+    "UAU":"Y", "UAC":"Y", "UAA":"STOP", "UAG":"STOP",
+    "UGU":"C", "UGC":"C", "UGA":"STOP", "UGG":"W",
+    "CUU":"L", "CUC":"L", "CUA":"L", "CUG":"L",
+    "CCU":"P", "CCC":"P", "CCA":"P", "CCG":"P",
+    "CAU":"H", "CAC":"H", "CAA":"Q", "CAG":"Q",
+    "CGU":"R", "CGC":"R", "CGA":"R", "CGG":"R",
+    "AUU":"I", "AUC":"I", "AUA":"I", "AUG":"M",
+    "ACU":"T", "ACC":"T", "ACA":"T", "ACG":"T",
+    "AAU":"N", "AAC":"N", "AAA":"K", "AAG":"K",
+    "AGU":"S", "AGC":"S", "AGA":"R", "AGG":"R",
+    "GUU":"V", "GUC":"V", "GUA":"V", "GUG":"V",
+    "GCU":"A", "GCC":"A", "GCA":"A", "GCG":"A",
+    "GAU":"D", "GAC":"D", "GAA":"E", "GAG":"E",
+    "GGU":"G", "GGC":"G", "GGA":"G", "GGG":"G",}
+
+	protein = ''
+	# find the start codon and proceed until a 'STOP'
+	start = mRNA.find('AUG')
+	if start != -1:
+		while start+2 < len(mRNA):
+			protein += codon_map[mRNA[start:start+3]]
+			start += 3
+		protein = protein[:protein.find('STOP')]
+	print protein
+
+if __name__ == "__main__":
+	""" Parse the command line arguments """
+	parser = argparse.ArgumentParser()
+	parser.add_argument("-r", "--mRNA", type=argparse.FileType('r'), default=sys.stdin)
+	args = vars(parser.parse_args())
+
+	""" Run the main method """
+	translate(args)

rabix-cli/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.rabix</groupId>
 		<artifactId>rabix</artifactId>
-		<version>1.0.4</version>
+		<version>1.0.5</version>
 	</parent>
 	<artifactId>rabix-cli</artifactId>
 	<name>rabix-cli</name>