added downsampled chr22 RNA workflow

RNA/GDC_mRNA_multi_dr32chr22/widgets/GDC_mRNA_multi_dr32chr22/GDC_mRNA_multi_dr32_fpkm_fpkm/Dockerfiles/Dockerfile

@@ -0,0 +1,4 @@
+FROM alpine:3.12.1
+MAINTAINER Hong Hung
+RUN apk add --update perl && rm -rf /var/cache/apk/*
+COPY fpkm.pl /usr/local/bin/fpkm.pl

RNA/GDC_mRNA_multi_dr32chr22/widgets/GDC_mRNA_multi_dr32chr22/GDC_mRNA_multi_dr32_fpkm_fpkm/Dockerfiles/fpkm.pl

@@ -0,0 +1,97 @@
+#!/usr/bin/perl
+#Ling-Hong Hung 2020
+my ($gencodeFile,$sampleFile)=@ARGV;
+my $STARFLAG = $ENV{'STARFLAG'};
+print STDERR "Opening gene code summary $gencodeFile\n";
+open (FIL, $gencodeFile) || die;
+my $line=<FIL>;
+my %pcLength;
+my %geneLength;
+my $basename=$sampleFile;
+if (substr($sampleFile,-4,1) eq "."){
+	$basename=substr($sampleFile,0,-4);
+}
+while (defined(my $line=<FIL>)){
+	my @parts=split(/\t/,$line);
+	my $name=$parts[0];
+	my $len=$parts[10];
+	$geneLength{$name}=$len;
+	if ($parts[6] eq "protein_coding"){
+	    $pcLength{$name}=$len;	
+	} 
+}
+#For STAR counts - the first four lines are information lines and there is no header
+#The columns are geneID unstrandedCounts 1stReadCounts 2ndReadCounts
+open (FIL, $sampleFile) || die "can't open $sampleFile";
+my $header=<FIL>;
+if($STARFLAG){
+	$header+=<FIL>;
+	$header+=<FIL>;
+	$header+=<FIL>;
+}
+my @names;
+my @pcSums;
+my @uq75s;
+my @counts;
+# 3 fields if STAR
+my $nfields=3;
+unless ($STARFLAG){
+	my @parts=split(/\t/,"$header");
+	$nfields=$#parts;
+}
+
+while (defined(my $line=<FIL>)){
+	chomp($line);
+	my @parts=split(/\t/,$line);
+	if ($#parts != $nfields){
+		next;
+	}
+	my $name=$parts[0];
+	my $length=$geneLength{$name};
+	if($length){
+		push(@names,$name);
+		if($pcLength{$name}){
+			foreach my $i (1..$nfields){
+				push(@{$counts[$i-1]},$parts[$i]);
+				$pcSums[$i-1]+=$parts[$i];
+			}			
+		}
+		else{
+			foreach my $i (1..$nfields){
+				push(@{$counts[$i-1]},$parts[$i]);
+			}
+		}
+	}
+}
+foreach my $i (0..$nfields-1){
+ my(@sorted)=sort{$a <=> $b} @{$counts[$i]};
+ my $uq75index=sprintf "%d",($#sorted+1)*.75;
+ $uq75s[$i]=$sorted[$uq75index];
+}
+open (fpkmfp,">$basename\_fpkm.tsv") || die;
+open (fpkmUQfp,">$basename\_fpkmUQ.tsv") || die;
+open (countsfp,">$basename\_counts.tsv") || die;
+print countsfp "$header";
+print fpkmfp "$header";
+print fpkmUQfp "$header";
+foreach my $i (0..$#names){
+	my $name=$names[$i];
+	my $length=$geneLength{$name};
+	print countsfp "$names[$i]";
+	print fpkmfp "$names[$i]";
+	print fpkmUQfp "$names[$i]";
+	foreach my $j (0..$nfields-1){
+		my $counts=$counts[$j][$i];
+		my $fpkmUQ="NA";
+		my $fpkm=$counts*1000000000/($length*$pcSums[$j]);
+		if ($uq75s[$j]){
+			$fpkmUQ=$counts*1000000000/($length*$uq75s[$j]);
+		}
+		print countsfp "\t$counts";
+		print fpkmfp "\t$fpkm";
+		print fpkmUQfp "\t$fpkmUQ";
+	}
+	print countsfp "\n";
+	print fpkmfp "\n";
+	print fpkmUQfp "\n";
+}

RNA/GDC_mRNA_multi_dr32chr22/widgets/GDC_mRNA_multi_dr32chr22/GDC_mRNA_multi_dr32_fpkm_fpkm/GDC_mRNA_multi_dr32_fpkm_fpkm.attrs

@@ -0,0 +1 @@
+{"autoMap": null, "buildCommand": null, "command": null, "description": null, "docker_image_name": null, "docker_image_tag": null, "icon": null, "inputs": null, "name": "GDC_mRNA_multi_dr32_fpkm_fpkm", "outputs": null, "parameters": null, "priority": null, "volumes": null, "runDockerMap": null}

RNA/GDC_mRNA_multi_dr32chr22/widgets/GDC_mRNA_multi_dr32chr22/GDC_mRNA_multi_dr32_fpkm_fpkm/GDC_mRNA_multi_dr32_fpkm_fpkm.json

@@ -0,0 +1 @@
+{"name": "GDC_mRNA_multi_dr32_fpkm_fpkm", "description": "Calculates fpkm and fpkm-UC using gdc formula", "docker_image_name": "biodepot/fpkm", "docker_image_tag": "latest", "priority": "10", "icon": null, "inputs": {"py/reduce": [{"py/type": "collections.OrderedDict"}, {"py/tuple": []}, null, null, {"py/tuple": [{"py/tuple": ["geneinfofile", {"callback": null, "type": {"py/type": "builtins.str"}}]}, {"py/tuple": ["countsfile", {"callback": null, "type": {"py/type": "builtins.str"}}]}, {"py/tuple": ["countsfilecreated", {"callback": null, "type": {"py/type": "builtins.str"}}]}]}]}, "outputs": {"py/reduce": [{"py/type": "collections.OrderedDict"}, {"py/tuple": []}, null, null, {"py/tuple": [{"py/tuple": ["countsfile", {"default": null, "type": {"py/type": "builtins.str"}}]}]}]}, "volumes": null, "ports": null, "parameters": {"py/reduce": [{"py/type": "collections.OrderedDict"}, {"py/tuple": []}, null, null, {"py/tuple": [{"py/tuple": ["geneinfofile", {"default": "/data/gencode.gene.info.v22.tsv", "flag": null, "argument": true, "label": "Gene info file", "type": "file"}]}, {"py/tuple": ["countsfile", {"flag": null, "argument": true, "label": "Counts file", "type": "file"}]}, {"py/tuple": ["starformat", {"flag": null, "label": "STAR Count format", "type": "bool", "env": "STARFLAG"}]}]}]}, "command": ["fpkm.pl "], "autoMap": true, "runDockerMap": null, "persistentSettings": "all", "requiredParameters": ["geneinfofile", "countsfile"]}

RNA/GDC_mRNA_multi_dr32chr22/widgets/GDC_mRNA_multi_dr32chr22/GDC_mRNA_multi_dr32_fpkm_fpkm/GDC_mRNA_multi_dr32_fpkm_fpkm.py

@@ -0,0 +1,61 @@
+import os
+import glob
+import sys
+import functools
+import jsonpickle
+from collections import OrderedDict
+from Orange.widgets import widget, gui, settings
+import Orange.data
+from Orange.data.io import FileFormat
+from DockerClient import DockerClient
+from BwBase import OWBwBWidget, ConnectionDict, BwbGuiElements, getIconName, getJsonName
+from PyQt5 import QtWidgets, QtGui
+
+class OWGDC_mRNA_multi_dr32_fpkm_fpkm(OWBwBWidget):
+    name = "GDC_mRNA_multi_dr32_fpkm_fpkm"
+    description = "Calculates fpkm and fpkm-UC using gdc formula"
+    priority = 10
+    icon = getIconName(__file__,"normalize_pl.png")
+    want_main_area = False
+    docker_image_name = "biodepot/fpkm"
+    docker_image_tag = "latest"
+    inputs = [("geneinfofile",str,"handleInputsgeneinfofile"),("countsfile",str,"handleInputscountsfile"),("countsfilecreated",str,"handleInputscountsfilecreated")]
+    outputs = [("countsfile",str)]
+    pset=functools.partial(settings.Setting,schema_only=True)
+    runMode=pset(0)
+    exportGraphics=pset(False)
+    runTriggers=pset([])
+    triggerReady=pset({})
+    inputConnectionsStore=pset({})
+    optionsChecked=pset({})
+    geneinfofile=pset("/data/gencode.gene.info.v22.tsv")
+    countsfile=pset(None)
+    starformat=pset(False)
+    def __init__(self):
+        super().__init__(self.docker_image_name, self.docker_image_tag)
+        with open(getJsonName(__file__,"GDC_mRNA_multi_dr32_fpkm_fpkm")) as f:
+            self.data=jsonpickle.decode(f.read())
+            f.close()
+        self.initVolumes()
+        self.inputConnections = ConnectionDict(self.inputConnectionsStore)
+        self.drawGUI()
+    def handleInputsgeneinfofile(self, value, *args):
+        if args and len(args) > 0: 
+            self.handleInputs("geneinfofile", value, args[0][0], test=args[0][3])
+        else:
+            self.handleInputs("inputFile", value, None, False)
+    def handleInputscountsfile(self, value, *args):
+        if args and len(args) > 0: 
+            self.handleInputs("countsfile", value, args[0][0], test=args[0][3])
+        else:
+            self.handleInputs("inputFile", value, None, False)
+    def handleInputscountsfilecreated(self, value, *args):
+        if args and len(args) > 0: 
+            self.handleInputs("countsfilecreated", value, args[0][0], test=args[0][3])
+        else:
+            self.handleInputs("inputFile", value, None, False)
+    def handleOutputs(self):
+        outputValue=None
+        if hasattr(self,"countsfile"):
+            outputValue=getattr(self,"countsfile")
+        self.send("countsfile", outputValue)

RNA/GDC_mRNA_multi_dr32chr22/widgets/GDC_mRNA_multi_dr32chr22/GDC_mRNA_multi_dr32_fpkm_fpkm/GDC_mRNA_multi_dr32_fpkm_fpkm.states

@@ -0,0 +1 @@
+{"addBuildDate": [true, true], "autoMap": [true, true], "buildCommand": [true, ""], "command": [true, "fpkm.pl "], "description": [[null, null], [true, "description:"], [true, "Calculates fpkm and fpkm-UC using gdc formula"]], "docker_image_name": [[null, null], [true, "docker_image_name:"], [true, "biodepot/fpkm"]], "docker_image_tag": [[null, null], [true, "docker_image_tag:"], [true, "latest"]], "icon": [[null, null], [true, "icon:"], [true, ""]], "inputs": [[[[null, null], [true, "Name"], [true, "geneinfofile"]], [[true, false], [true, "callback"], [false, ""]], [[true, 0, ["str", "dict", "Orange.data.Table"]], [true, "Type:"]]], [[[null, null], [true, "Name"], [true, "countsfile"]], [[true, false], [true, "callback"], [false, ""]], [[true, 0, ["str", "dict", "Orange.data.Table"]], [true, "Type:"]]], [[[null, null], [true, "Name"], [true, "countsfilecreated"]], [[true, false], [true, "callback"], [false, ""]], [[true, 0, ["str", "dict", "Orange.data.Table"]], [true, "Type:"]]]], "outputs": [[[[null, null], [true, "Name"], [true, "countsfile"]], [[true, false], [true, "Default value"], [false, ""]], [[true, 0, ["str", "dict", "Orange.data.Table"]], [true, "Type:"]]]], "parameters": [[[[null, null], [true, "Name"], [true, "geneinfofile"]], [[true, 1, ["str", "file", "file list", "directory", "directory list", "bool", "bool list", "text list", "int", "int list", "double", "double list", "patternQuery"]], [true, "Type:"]], [[true, false], [true, "flag"], [false, ""]], [true, true], [[true, false], [true, "env"], [false, ""]], [[true, true], [true, "label"], [true, "Gene info file"]], [[true, true], [true, "default"], [true, "/data/gencode.gene.info.v22.tsv"]], [[true, false], [true, "group"], [false, ""]], [true, false]], [[[null, null], [true, "Name"], [true, "countsfile"]], [[true, 1, ["str", "file", "file list", "directory", "directory list", "bool", "bool list", "text list", "int", "int list", "double", "double list", "patternQuery"]], [true, "Type:"]], [[true, false], [true, "flag"], [false, ""]], [true, true], [[true, false], [true, "env"], [false, ""]], [[true, true], [true, "label"], [true, "Counts file"]], [[true, false], [true, "default"], [false, ""]], [[true, false], [true, "group"], [false, ""]], [true, false]], [[[null, null], [true, "Name"], [true, "starformat"]], [[true, 5, ["str", "file", "file list", "directory", "directory list", "bool", "bool list", "text list", "int", "int list", "double", "double list", "patternQuery"]], [true, "Type:"]], [[true, false], [true, "flag"], [false, ""]], [true, false], [[true, true], [true, "env"], [true, "STARFLAG"]], [[true, true], [true, "label"], [true, "STAR Count format"]], [[true, false], [true, "default"], [false, ""]], [[true, false], [true, "group"], [false, ""]], [true, true]]], "priority": [[null, null], [true, "priority:"], [true, "10"]], "name": "GDC_mRNA_multi_dr32_fpkm_fpkm", "runDockerMap": [true, false]}

RNA/GDC_mRNA_multi_dr32chr22/widgets/GDC_mRNA_multi_dr32chr22/StarFusion/Dockerfiles/Dockerfile

@@ -0,0 +1,26 @@
+FROM debian:buster-slim
+Maintainer Ling-Hong Hung
+ENV DEBIAN_FRONTEND=noninteractive
+ENV STAR_FUSION_VERSION 1.9.0
+ENV SAMTOOLS_VERSION 1.9
+ENV HTSLIB_VERSION 1.9
+
+RUN apt-get update && apt-get install -y libgomp1 libbz2-dev wget build-essential libdb-dev libz-dev libcurl4-openssl-dev  liblzma-dev libncurses5-dev \
+    && wget -qO- https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 | tar -xjvf - \
+    && cd /samtools-${SAMTOOLS_VERSION} && ./configure &&  make  \
+    && mv /samtools-${SAMTOOLS_VERSION}/samtools /bin/ \
+    && cd htslib-${HTSLIB_VERSION}/ && ./configure && make \
+    && mv htsfile libhts.so* tabix bgzip /bin \
+    && cd /root && rm -rf /samtools* \
+    && wget -O - http://cpanmin.us | perl - --self-upgrade \
+    && cpanm Data::Dumper FindBin DB_File URI::Escape Set::IntervalTree Carp::Assert JSON::XS PerlIO::gzip \
+    && wget -qO- https://github.com/STAR-Fusion/STAR-Fusion/releases/download/STAR-Fusion-v${STAR_FUSION_VERSION}/STAR-Fusion.v${STAR_FUSION_VERSION}.FULL.tar.gz \
+    | tar -xzvf - \
+    && mv STAR-Fusion.v${STAR_FUSION_VERSION} STAR-Fusion \
+    && apt-get remove -y wget build-essential \
+    && apt-get clean -y \
+    && apt-get autoremove -y \
+    && rm -rf /var/lib/apt/lists/*
+RUN touch /usr/local/bin/STAR
+RUN chmod +x /usr/local/bin/STAR
+RUN sed -i 's/\&check_compatible_STAR/\#&check_compatible_STAR/' /root/STAR-Fusion/STAR-Fusion

RNA/GDC_mRNA_multi_dr32chr22/widgets/GDC_mRNA_multi_dr32chr22/StarFusion/StarFusion.attrs

@@ -0,0 +1 @@
+{"autoMap": null, "buildCommand": null, "command": null, "description": null, "docker_image_name": null, "docker_image_tag": null, "icon": null, "inputs": null, "name": "StarFusion", "outputs": null, "parameters": null, "priority": null, "volumes": null, "runDockerMap": null}

RNA/GDC_mRNA_multi_dr32chr22/widgets/GDC_mRNA_multi_dr32chr22/StarFusion/StarFusion.json

@@ -0,0 +1 @@
+{"name": "StarFusion", "description": "Detect gene fusions from STAR junctions", "docker_image_name": "biodepot/star-fusion", "docker_image_tag": "1.9.0", "priority": "10", "icon": null, "inputs": {"py/reduce": [{"py/type": "collections.OrderedDict"}, {"py/tuple": []}, null, null, {"py/tuple": [{"py/tuple": ["genomelibdir", {"callback": null, "type": {"py/type": "builtins.str"}}]}, {"py/tuple": ["chimeric", {"callback": null, "type": {"py/type": "builtins.str"}}]}, {"py/tuple": ["Trigger", {"callback": null, "type": {"py/type": "builtins.str"}}]}]}]}, "outputs": {"py/reduce": [{"py/type": "collections.OrderedDict"}, {"py/tuple": []}, null, null, {"py/tuple": [{"py/tuple": ["outputdir", {"default": null, "type": {"py/type": "builtins.str"}}]}]}]}, "volumes": null, "ports": null, "parameters": {"py/reduce": [{"py/type": "collections.OrderedDict"}, {"py/tuple": []}, null, null, {"py/tuple": [{"py/tuple": ["chimeric", {"flag": "-J", "label": "Chimeric.out.junction file", "type": "file"}]}, {"py/tuple": ["genomelibdir", {"flag": "--genome_lib_dir", "label": "Genome lib directory", "type": "directory"}]}, {"py/tuple": ["cpu", {"flag": "--CPU", "label": "Number of threads", "type": "int"}]}, {"py/tuple": ["outputdir", {"default": "STAR-Fusion_outdir", "flag": "-O ", "label": "Output directory", "type": "directory"}]}, {"py/tuple": ["fullusage", {"flag": "--show_full_usage_info", "label": "Provide full usage info", "type": "bool"}]}]}]}, "command": ["/root/STAR-Fusion/STAR-Fusion "], "autoMap": true, "runDockerMap": null, "persistentSettings": "all", "requiredParameters": ["chimeric", "genomelibdir"]}

RNA/GDC_mRNA_multi_dr32chr22/widgets/GDC_mRNA_multi_dr32chr22/StarFusion/StarFusion.py

@@ -0,0 +1,63 @@
+import os
+import glob
+import sys
+import functools
+import jsonpickle
+from collections import OrderedDict
+from Orange.widgets import widget, gui, settings
+import Orange.data
+from Orange.data.io import FileFormat
+from DockerClient import DockerClient
+from BwBase import OWBwBWidget, ConnectionDict, BwbGuiElements, getIconName, getJsonName
+from PyQt5 import QtWidgets, QtGui
+
+class OWStarFusion(OWBwBWidget):
+    name = "StarFusion"
+    description = "Detect gene fusions from STAR junctions"
+    priority = 10
+    icon = getIconName(__file__,"starfusion.png")
+    want_main_area = False
+    docker_image_name = "biodepot/star-fusion"
+    docker_image_tag = "1.9.0"
+    inputs = [("genomelibdir",str,"handleInputsgenomelibdir"),("chimeric",str,"handleInputschimeric"),("Trigger",str,"handleInputsTrigger")]
+    outputs = [("outputdir",str)]
+    pset=functools.partial(settings.Setting,schema_only=True)
+    runMode=pset(0)
+    exportGraphics=pset(False)
+    runTriggers=pset([])
+    triggerReady=pset({})
+    inputConnectionsStore=pset({})
+    optionsChecked=pset({})
+    chimeric=pset(None)
+    genomelibdir=pset(None)
+    cpu=pset(None)
+    outputdir=pset("STAR-Fusion_outdir")
+    fullusage=pset(False)
+    def __init__(self):
+        super().__init__(self.docker_image_name, self.docker_image_tag)
+        with open(getJsonName(__file__,"StarFusion")) as f:
+            self.data=jsonpickle.decode(f.read())
+            f.close()
+        self.initVolumes()
+        self.inputConnections = ConnectionDict(self.inputConnectionsStore)
+        self.drawGUI()
+    def handleInputsgenomelibdir(self, value, *args):
+        if args and len(args) > 0: 
+            self.handleInputs("genomelibdir", value, args[0][0], test=args[0][3])
+        else:
+            self.handleInputs("inputFile", value, None, False)
+    def handleInputschimeric(self, value, *args):
+        if args and len(args) > 0: 
+            self.handleInputs("chimeric", value, args[0][0], test=args[0][3])
+        else:
+            self.handleInputs("inputFile", value, None, False)
+    def handleInputsTrigger(self, value, *args):
+        if args and len(args) > 0: 
+            self.handleInputs("Trigger", value, args[0][0], test=args[0][3])
+        else:
+            self.handleInputs("inputFile", value, None, False)
+    def handleOutputs(self):
+        outputValue=None
+        if hasattr(self,"outputdir"):
+            outputValue=getattr(self,"outputdir")
+        self.send("outputdir", outputValue)

RNA/GDC_mRNA_multi_dr32chr22/widgets/GDC_mRNA_multi_dr32chr22/StarFusion/StarFusion.states

@@ -0,0 +1 @@
+{"addBuildDate": [true, true], "autoMap": [true, true], "buildCommand": [true, ""], "command": [true, "/root/STAR-Fusion/STAR-Fusion "], "description": [[null, null], [true, "description:"], [true, "Detect gene fusions from STAR junctions"]], "docker_image_name": [[null, null], [true, "docker_image_name:"], [true, "biodepot/star-fusion"]], "docker_image_tag": [[null, null], [true, "docker_image_tag:"], [true, "1.9.0"]], "icon": [[null, null], [true, "icon:"], [true, ""]], "inputs": [[[[null, null], [true, "Name"], [true, "genomelibdir"]], [[true, false], [true, "callback"], [false, ""]], [[true, 0, ["str", "dict", "Orange.data.Table"]], [true, "Type:"]]], [[[null, null], [true, "Name"], [true, "chimeric"]], [[true, false], [true, "callback"], [false, ""]], [[true, 0, ["str", "dict", "Orange.data.Table"]], [true, "Type:"]]], [[[null, null], [true, "Name"], [true, "Trigger"]], [[true, false], [true, "callback"], [false, ""]], [[true, 0, ["str", "dict", "Orange.data.Table"]], [true, "Type:"]]]], "outputs": [[[[null, null], [true, "Name"], [true, "outputdir"]], [[true, false], [true, "Default value"], [false, ""]], [[true, 0, ["str", "dict", "Orange.data.Table"]], [true, "Type:"]]]], "parameters": [[[[null, null], [true, "Name"], [true, "chimeric"]], [[true, 1, ["str", "file", "file list", "directory", "directory list", "bool", "bool list", "text list", "int", "int list", "double", "double list", "patternQuery"]], [true, "Type:"]], [[true, true], [true, "flag"], [true, "-J"]], [true, false], [[true, false], [true, "env"], [false, ""]], [[true, true], [true, "label"], [true, "Chimeric.out.junction file"]], [[true, false], [true, "default"], [false, ""]], [[true, false], [true, "group"], [false, ""]], [true, false]], [[[null, null], [true, "Name"], [true, "genomelibdir"]], [[true, 3, ["str", "file", "file list", "directory", "directory list", "bool", "bool list", "text list", "int", "int list", "double", "double list", "patternQuery"]], [true, "Type:"]], [[true, true], [true, "flag"], [true, "--genome_lib_dir"]], [true, false], [[true, false], [true, "env"], [false, ""]], [[true, true], [true, "label"], [true, "Genome lib directory"]], [[true, false], [true, "default"], [false, ""]], [[true, false], [true, "group"], [false, ""]], [true, false]], [[[null, null], [true, "Name"], [true, "cpu"]], [[true, 8, ["str", "file", "file list", "directory", "directory list", "bool", "bool list", "text list", "int", "int list", "double", "double list", "patternQuery"]], [true, "Type:"]], [[true, true], [true, "flag"], [true, "--CPU"]], [true, false], [[true, false], [true, "env"], [false, ""]], [[true, true], [true, "label"], [true, "Number of threads"]], [[true, false], [true, "default"], [false, ""]], [[true, false], [true, "group"], [false, ""]], [true, true]], [[[null, null], [true, "Name"], [true, "outputdir"]], [[true, 3, ["str", "file", "file list", "directory", "directory list", "bool", "bool list", "text list", "int", "int list", "double", "double list", "patternQuery"]], [true, "Type:"]], [[true, true], [true, "flag"], [true, "-O "]], [true, false], [[true, false], [true, "env"], [false, ""]], [[true, true], [true, "label"], [true, "Output directory"]], [[true, true], [true, "default"], [true, "STAR-Fusion_outdir"]], [[true, false], [true, "group"], [false, ""]], [true, true]], [[[null, null], [true, "Name"], [true, "fullusage"]], [[true, 5, ["str", "file", "file list", "directory", "directory list", "bool", "bool list", "text list", "int", "int list", "double", "double list", "patternQuery"]], [true, "Type:"]], [[true, true], [true, "flag"], [true, "--show_full_usage_info"]], [true, false], [[true, false], [true, "env"], [false, ""]], [[true, true], [true, "label"], [true, "Provide full usage info"]], [[true, false], [true, "default"], [false, ""]], [[true, false], [true, "group"], [false, ""]], [true, true]]], "priority": [[null, null], [true, "priority:"], [true, "10"]], "name": "StarFusion", "runDockerMap": [true, false]}

RNA/GDC_mRNA_multi_dr32chr22/widgets/GDC_mRNA_multi_dr32chr22/Start/Dockerfiles/Dockerfile

@@ -0,0 +1,4 @@
+FROM alpine:3.12.1
+MAINTAINER Hong Hung
+RUN apk update upgrade --no-cache && apk add bash && rm -rf /var/cache/apk* 
+COPY start.sh /usr/local/bin/.

RNA/GDC_mRNA_multi_dr32chr22/widgets/GDC_mRNA_multi_dr32chr22/Start/Dockerfiles/start.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+printenv
+
+mkdir -p $work_dir || exit 1
+mkdir -p $genome_dir || exit 1