tested quitBwb on mac

BioDepot · Jan 24, 2024 · 6d3fae5 · 6d3fae5
1 parent 87e2da8
commit 6d3fae5
Show file tree

Hide file tree

Showing 50 changed files with 1,506 additions and 0 deletions.
diff --git a/nfcore_star_salmon/nfcore_star_salmon.ows b/nfcore_star_salmon/nfcore_star_salmon.ows
@@ -0,0 +1,23 @@
+<?xml version="1.0" ?><scheme description="" title="nfcore-star-salmon" version="2.0">
+	<nodes>
+		<node id="0" name="starAlign" position="(489.0, 178.0)" project_name="nfcore-star-salmon" qualified_name="nfcore_star_salmon.OWstarAlign.OWstarAlign" title="starAlign" version=""/>
+		<node id="1" name="starIndex" position="(361.0, 179.0)" project_name="nfcore-star-salmon" qualified_name="nfcore_star_salmon.OWstarIndex.OWstarIndex" title="starIndex" version=""/>
+		<node id="2" name="downloadURL" position="(168.0, 159.0)" project_name="nfcore-star-salmon" qualified_name="nfcore_star_salmon.OWdownloadURL.OWdownloadURL" title="downloadURL" version=""/>
+		<node id="3" name="S3_download" position="(132.0, 248.0)" project_name="nfcore-star-salmon" qualified_name="nfcore_star_salmon.OWS3_download.OWS3_download" title="S3_download" version=""/>
+		<node id="4" name="igv" position="(623.0, 165.0)" project_name="nfcore-star-salmon" qualified_name="nfcore_star_salmon.OWigv.OWigv" title="igv" version=""/>
+		<node id="5" name="fastqc" position="(728.0, 157.0)" project_name="nfcore-star-salmon" qualified_name="nfcore_star_salmon.OWfastqc.OWfastqc" title="fastqc" version=""/>
+		<node id="6" name="salmon" position="(307.0, 335.0)" project_name="nfcore-star-salmon" qualified_name="nfcore_star_salmon.OWsalmon.OWsalmon" title="Salmon quantify" version=""/>
+	</nodes>
+	<links/>
+	<annotations/>
+	<thumbnail/>
+	<node_properties>
+		<properties format="literal" node_id="0">{'alignEndsProtrude': ['0', 'ConcordantPair'], 'alignEndsType': 'Local', 'alignIntronMax': 0, 'alignIntronMin': 21, 'alignMatesGapMax': 0, 'alignSJDBoverhangMin': 3, 'alignSJoverhangMin': 5, 'alignSJstitchMismatchNmax': 0, 'alignSoftClipAtReferenceEnds': 'Yes', 'alignSplicedMateMapLmin': 0, 'alignSplicedMateMapLminOverLmate': 0.66, 'alignTranscriptsPerReadNmax': 10000, 'alignTranscriptsPerWindowNmax': 100, 'alignWindowsPerReadNmax': 10000, 'apelist': False, 'bamRemoveDuplicatesMate2basesN': 0, 'bamRemoveDuplicatesType': '', 'chimFilter': 'banGenomicN', 'chimJunctionOverhangMin': 20, 'chimOutType': 'SeparateSAMold', 'chimScoreDropMax': 20, 'chimScoreJunctionNonGTAG': -1, 'chimScoreMin': 0, 'chimScoreSeparation': 10, 'chimSegmentMin': 0, 'chimSegmentReadGapMax': 0, 'clip3pAdapterMMp': ['0.1'], 'clip3pAdapterSeq': [], 'clip3pAfterAdapterNbases': ['0'], 'clip3pNbases': ['0'], 'clip5pNbases': ['0'], 'controlAreaVisible': True, 'exportGraphics': False, 'genomeDir': '/data/GenomeDir', 'genomeLoad': 'NoSharedMemory', 'inputConnectionsStore': {}, 'iterate': False, 'iterateSettings': {'iterableAttrs': ['readFilesIn', 'clip3pNbases', 'clip5pNbases', 'clip3pAdapterSeq', 'clip3pAdapterMMp', 'clip3pAfterAdapterNbases', 'alignEndsProtrude']}, 'limitIObufferSize': 150000000, 'limitOutSAMoneReadBytes': 100000, 'multipleSample': False, 'nWorkers': 1, 'optionsChecked': {'apelist': False, 'spelist': False, 'parametersFiles': False, 'sysShell': False, 'runThreadN': False, 'runRNGseed': False, 'readFilesCommand': False, 'readMapNumber': False, 'readMatesLengthsIn': False, 'readNameSeparator': False, 'clip3pNbases': False, 'clip5pNbases': False, 'clip3pAdapterSeq': False, 'clip3pAdapterMMp': False, 'clip3pAfterAdapterNbases': False, 'limitIObufferSize': False, 'limitOutSAMoneReadBytes': False, 'outTmpDir': False, 'outStd': False, 'outReadsUnmapped': False, 'outMultimapperOrder': False, 'outSAMtype': False, 'outSAMmode': False, 'outSAMstrandField': False, 'outSAMattributes': False, 'outSAMattrIHstart': False, 'outSAMunmapped': False, 'outSAMorder': False, 'outSAMprimaryFlag': False, 'outSAMreadID': False, 'outSAMmapqUnique': False, 'outSAMflagOR': False, 'outSAMflagAND': False, 'outSAMattrRGline': False, 'outSAMheaderHD': False, 'outSAMheaderPG': False, 'outSAMheaderCommentFile': False, 'outSAMfilter': False, 'outSAMmultNmax': False, 'outBAMcompression': False, 'outBAMsortingThreadN': False, 'bamRemoveDuplicatesType': False, 'bamRemoveDuplicatesMate2basesN': False, 'outWigType': False, 'outWigStrand': False, 'outWigReferencesPrefix': False, 'outWigNorm': False, 'outFilterType': False, 'outFilterMultimapScoreRange': False, 'outFilterMultimapNmax': False, 'outFilterMismatchNmax': False, 'outFilterMismatchNoverLmax ': False, 'outFilterMismatchNoverReadLmax': False, 'outFilterScoreMin': False, 'outFilterScoreMinOverLread': False, 'outFilterMatchNmin': False, 'outFilterMatchNminOverLread': False, 'outFilterIntronMotifs': False, 'scoreGap': False, 'scoreGapNoncan': False, 'scoreGapGCAG': False, 'scoreGapATAC': False, 'scoreGenomicLengthLog2scale': False, 'scoreDelOpen': False, 'scoreDelBase': False, 'scoreInsOpen': False, 'scoreInsBase': False, 'scoreStitchSJshift': False, 'seedSearchStartLmax': False, 'seedSearchStartLmaxOverLread': False, 'seedSearchLmax': False, 'seedMultimapNmax': False, 'seedPerReadNmax': False, 'seedPerWindowNmax': False, 'seedNoneLociPerWindow': False, 'alignIntronMin': False, 'alignIntronMax': False, 'alignMatesGapMax': False, 'alignSJoverhangMin': False, 'alignSJstitchMismatchNmax': False, 'alignSJDBoverhangMin': False, 'alignSplicedMateMapLmin': False, 'alignSplicedMateMapLminOverLmate': False, 'alignWindowsPerReadNmax': False, 'alignTranscriptsPerWindowNmax': False, 'alignTranscriptsPerReadNmax': False, 'alignEndsType': False, 'alignEndsProtrude': False, 'alignSoftClipAtReferenceEnds': False, 'winAnchorMultimapNmax': False, 'winBinNbits': False, 'winAnchorDistNbins': False, 'winFlankNbins': False, 'winReadCoverageRelativeMin': False, 'winReadCoverageBasesMin': False, 'chimOutType': False, 'chimSegmentMin': False, 'chimScoreMin': False, 'chimScoreDropMax': False, 'chimScoreSeparation': False, 'chimScoreJunctionNonGTAG': False, 'chimJunctionOverhangMin': False, 'chimSegmentReadGapMax': False, 'chimFilter': False, 'quantMode': False, 'quantTranscriptomeBAMcompression': False, 'quantTranscriptomeBan': False, 'twopassMode': False, 'twopass1readsN ': False, 'genomeLoad': False, 'outputFilePrefix': False, 'multipleSample': False}, 'outBAMcompression': 1, 'outBAMsortingThreadN': 0, 'outFilterIntronMotifs': '', 'outFilterMatchNmin': 0, 'outFilterMatchNminOverLread': 0.66, 'outFilterMismatchNmax': 10, 'outFilterMismatchNoverLmax': 0.3, 'outFilterMismatchNoverReadLmax': 1.0, 'outFilterMultimapNmax': 10, 'outFilterMultimapScoreRange': 1, 'outFilterScoreMin': 0, 'outFilterScoreMinOverLread': 0.66, 'outFilterType': 'Normal', 'outMultimapperOrder': 'Old_2.4', 'outReadsUnmapped': '', 'outSAMattrIHstart': 1, 'outSAMattrRGline': '', 'outSAMattributes': 'Standard', 'outSAMfilter': '', 'outSAMflagAND': 65535, 'outSAMflagOR': 0, 'outSAMheaderCommentFile': '', 'outSAMheaderHD': '', 'outSAMheaderPG': '', 'outSAMmapqUnique': 255, 'outSAMmode': 'Full', 'outSAMmultNmax': -1, 'outSAMorder': 'Paired', 'outSAMprimaryFlag': 'OneBestScore', 'outSAMreadID': 'Standard', 'outSAMstrandField': '', 'outSAMtype': 'SAM', 'outSAMunmapped': '', 'outStd': 'Log', 'outTmpDir': '', 'outWigNorm': 'RPM', 'outWigReferencesPrefix': '', 'outWigStrand': 'Stranded', 'outWigType': '', 'outputDir': '', 'outputFilePrefix': '', 'parametersFiles': '', 'quantMode': '', 'quantTranscriptomeBAMcompression': 1, 'quantTranscriptomeBan': 'IndelSoftclipSingleend', 'readFilesCommand': '', 'readFilesIn': [], 'readMapNumber': -1, 'readMatesLengthsIn': 'NotEqual', 'readNameSeparator': '/', 'runMode': 0, 'runRNGseed': 777, 'runThreadN': 1, 'runTriggers': [], 'savedWidgetGeometry': None, 'scoreDelBase': -2, 'scoreDelOpen': -2, 'scoreGap': 0, 'scoreGapATAC': -8, 'scoreGapGCAG': -4, 'scoreGapNoncan': -8, 'scoreGenomicLengthLog2scale': -0.25, 'scoreInsBase': -2, 'scoreInsOpen': -2, 'scoreStitchSJshift': 1, 'seedMultimapNmax': 10000, 'seedNoneLociPerWindow': 10, 'seedPerReadNmax': 1000, 'seedPerWindowNmax': 50, 'seedSearchLmax': 0, 'seedSearchStartLmax': 50, 'seedSearchStartLmaxOverLread': 1.0, 'spelist': False, 'sysShell': '/bin/sh', 'triggerReady': {}, 'twopass1readsN': -1, 'twopassMode': '', 'useGpu': False, 'useScheduler': False, 'winAnchorDistNbins': 9, 'winAnchorMultimapNmax': 50, 'winBinNbits': 16, 'winFlankNbins': 4, 'winReadCoverageBasesMin': 0, 'winReadCoverageRelativeMin': 0.5, '__version__': 1}</properties>
+		<properties format="literal" node_id="1">{'controlAreaVisible': True, 'exportGraphics': False, 'genomeChrBinNbits': '18', 'genomeDir': '', 'genomeFastaFiles': [], 'genomeSAindexNbases': 14, 'genomeSAsparseD': 1, 'genomeSuffixLengthMax': -1, 'inputConnectionsStore': {}, 'iterate': False, 'iterateSettings': {'iterableAttrs': ['genomeFastaFiles', 'sjdbFileChrStartEnd ']}, 'nWorkers': 1, 'optionsChecked': {'genomeChrBinNbits': False, 'genomeSAindexNbases': False, 'genomeSAsparseD': False, 'genomeSuffixLengthMax': False, 'runThreadN': False, 'sjdbGTFfile': False, 'sjdbFileChrStartEnd ': False, 'sjdbGTFchrPrefix ': False, 'sjdbGTFfeatureExon': False, 'sjdbGTFtagExonParentTranscript': False, 'sjdbGTFtagExonParentGene': False, 'sjdbOverhang': False, 'sjdbScore': False, 'sjdbInsertSave ': False}, 'rmode': 'genomeGenerate', 'runMode': 0, 'runThreadN': 1, 'runTriggers': [], 'savedWidgetGeometry': None, 'sjdbFileChrStartEnd': [], 'sjdbGTFchrPrefix': 'chr', 'sjdbGTFfeatureExon': 'exon', 'sjdbGTFfile': '', 'sjdbGTFtagExonParentGene': 'gene_id', 'sjdbGTFtagExonParentTranscript': 'transcript_id', 'sjdbInsertSave': 'Basic', 'sjdbOverhang': 100, 'sjdbScore': 2, 'triggerReady': {}, 'useGpu': False, 'useScheduler': False, '__version__': 1}</properties>
+		<properties format="literal" node_id="2">{'URL': [], 'concatenateFile': '', 'controlAreaVisible': True, 'decompress': True, 'directory': '', 'exportGraphics': False, 'inputConnectionsStore': {}, 'iterate': False, 'iterateSettings': {'iterableAttrs': ['URL']}, 'nWorkers': 1, 'optionsChecked': {'decompress': False, 'concatenateFile': False}, 'runMode': 0, 'runTriggers': [], 'savedWidgetGeometry': None, 'triggerReady': {}, 'useGpu': False, 'useScheduler': False, '__version__': 1}</properties>
+		<properties format="literal" node_id="3">{'awsdir': '/data/.aws', 'bucket': 'myBucket', 'controlAreaVisible': True, 'dirs': [], 'downloadDir': '/data', 'exportGraphics': False, 'inputConnectionsStore': {}, 'iterate': False, 'iterateSettings': {'iterableAttrs': ['dirs']}, 'key': '', 'nWorkers': 1, 'nthreads': 0, 'optionsChecked': {'nthreads': False, 'key': False, 'secret': False, 'region': False}, 'region': 'us-east-2', 'runMode': 0, 'runTriggers': [], 'savedWidgetGeometry': None, 'secret': '', 'triggerReady': {}, 'useGpu': False, 'useScheduler': False, '__version__': 1}</properties>
+		<properties format="literal" node_id="4">{'autoDetermineRegions': True, 'batch': '', 'controlAreaVisible': True, 'exportGraphics': False, 'genome': 'hg38', 'inputConnectionsStore': {}, 'inputFile': [], 'iterate': False, 'iterateSettings': {'iterableAttrs': ['inputFile']}, 'nWorkers': 1, 'optionsChecked': {'genome': False, 'batch': False, 'autoDetermineRegions': False}, 'runMode': 0, 'runTriggers': [], 'savedWidgetGeometry': None, 'triggerReady': {}, 'useGpu': False, 'useScheduler': False, '__version__': 1}</properties>
+		<properties format="literal" node_id="5">{'controlAreaVisible': True, 'exportGraphics': False, 'inputConnectionsStore': {}, 'inputDir': '', 'inputFiles': [], 'iterate': False, 'iterateSettings': {'iterableAttrs': ['inputFiles']}, 'nWorkers': 1, 'optionsChecked': {'inputFiles': False, 'outputDir': False, 'inputDir': False}, 'outputDir': '', 'runMode': 0, 'runTriggers': [], 'savedWidgetGeometry': None, 'triggerReady': {}, 'useGpu': False, 'useScheduler': False, '__version__': 1}</properties>
+		<properties format="literal" node_id="6">{'command': 'quant', 'controlAreaVisible': True, 'exportGraphics': False, 'inputConnectionsStore': {}, 'iterate': False, 'iterateSettings': {'iterableAttrs': [], 'nWorkers': 1}, 'nWorkers': 1, 'optionsChecked': {'File': False}, 'runMode': 0, 'runTriggers': [], 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x02\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x07\x7f\x00\x00\x04\x19\x00\x00\x00\x00\x00\x00\x00\x18\x00\x00\x07\x7f\x00\x00\x04\x16\x00\x00\x00\x00\x02\x00\x00\x00\x07\x80', 'triggerReady': {}, 'useGpu': False, 'useScheduler': False, '__version__': 1}</properties>
+	</node_properties>
+</scheme>
diff --git a/nfcore_star_salmon/widgets/nfcore_star_salmon/S3_download/Dockerfiles/Dockerfile b/nfcore_star_salmon/widgets/nfcore_star_salmon/S3_download/Dockerfiles/Dockerfile
@@ -0,0 +1,6 @@
+FROM python:3.8.0-alpine3.10
+ARG CLI_VERSION=1.16.272
+RUN apk upgrade && apk add --no-cache nano bash zip jq
+RUN pip install --upgrade pip && pip install --no-cache-dir awscli==$CLI_VERSION && \
+    mkdir /root/.aws
+COPY download.sh /usr/local/bin/download.sh
diff --git a/nfcore_star_salmon/widgets/nfcore_star_salmon/S3_download/Dockerfiles/download.sh b/nfcore_star_salmon/widgets/nfcore_star_salmon/S3_download/Dockerfiles/download.sh
@@ -0,0 +1,113 @@
+#!/bin/bash
+
+awsdir=$1
+bucket=$2
+outputDir=$3
+
+error=0
+mkdir -p outputDir
+cp -r $awsdir/* /root/.aws || exit 1
+
+copy_wildcard(){
+ echo "parsing wildcards in $1"
+ local my_str=$1
+ local max_attempts=4
+ #if there is no / then we search from the base bucket
+ local my_glob=""
+ local wildcard=$my_str
+ if [[ $glob == */* ]]; then
+	#split into a glob (directory) and wildcard string
+	no_wc="${my_str%%['!'@#\$%^\&*()+]*}"
+	my_glob="${no_wc%/*}"/
+	wildcard="${my_str#$my_glob}"
+ fi
+ local command=(nice aws s3 cp --exclude "*" --include="$wildcard" --recursive s3://$bucket/$my_glob $outputDir)
+ local attempts
+ for attempts in {1..$max_attempts}; do
+	echo "${command[@]}"
+ 	if "${command[@]}" ; then
+   	return
+ 	fi
+ done
+ echo "error in ${command[@]}"
+ exit 1
+
+}
+
+copy_directory(){
+ echo "copying directory object $1"
+ local attempts
+ local max_attempts=2
+ local command=(nice aws s3 cp --recursive s3://$bucket/$1 $outputDir/$dest) 
+ for attempts in {1..$max_attempts}; do
+	echo "${command[@]}"
+ 	if "${command[@]}" ; then
+   	return
+ 	fi
+ done
+ echo "error in ${command[@]}"
+ exit 1
+
+}
+
+copy_file(){
+ echo "copying file object $1"
+ destination=basename $1
+ local attempts
+ local max_attempts=2
+ local command=(nice aws s3 cp s3://$bucket/$1 $outputDir/$dest) 
+ for attempts in {1..$max_attempts}; do
+	echo "${command[@]}"
+ 	if "${command[@]}" ; then
+   	return
+ 	fi
+ done
+ echo "error in ${command[@]}"
+ exit 1
+}
+
+copy(){
+   local my_glob=$1
+   echo "$my_glob"
+   if [[ $my_glob == *['!'@#\$%^\&*()+]* ]]; then
+     copy_wildcard $my_glob || error=1
+   elif [ "${my_glob: -1}" == "/" ]; then
+     copy_directory $my_glob || error=1
+   else
+    copy_file $my_glob || error=1
+   fi	
+}
+
+multiCopy(){
+ lasti=$((${#globs[@]} - 1))
+ for i in $(seq 0 ${lasti}); do
+  if ( mkdir $lockDir/lock$i 2> /dev/null ); then
+   glob=${globs[i]}
+   echo "thread $1 copying $glob"
+   copy $glob
+  fi
+ done
+}
+if [ -z $DIRS ] || [ "$DIRS" == "[]" ]; then
+    echo "no bucket object given to download"
+	exit 1
+fi
+globs=( $(echo $DIRS | jq -r '.[]') )
+
+if [ -z $nThreads ] || (( $nThreads == 1 )) || (( $nThreads == 0 )); then
+	#use single thread
+	echo "Using single thread"
+	for glob in "${globs[@]}"; do
+		copy $glob
+	done
+else
+	lockDir=/tmp/locks.$$
+	mkdir -p $lockDir
+	for i in $(seq 2 $nThreads); do
+	  multiCopy $i &
+	done
+	multiCopy 1 &
+	wait
+	rm -rf $lockDir
+fi
+exit $error
diff --git a/nfcore_star_salmon/widgets/nfcore_star_salmon/S3_download/S3_download.attrs b/nfcore_star_salmon/widgets/nfcore_star_salmon/S3_download/S3_download.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": "S3_upload", "outputs": null, "parameters": null, "priority": null, "volumes": null, "runDockerMap": null}
diff --git a/nfcore_star_salmon/widgets/nfcore_star_salmon/S3_download/S3_download.json b/nfcore_star_salmon/widgets/nfcore_star_salmon/S3_download/S3_download.json
@@ -0,0 +1 @@
+{"name": "S3_download", "description": "Enter and output a file", "docker_image_name": "biodepot/s3download", "docker_image_tag": "1.16.272__python_3.8.0__alpine-3.10__e2962454", "priority": "10", "icon": null, "inputs": {"py/reduce": [{"py/type": "collections.OrderedDict"}, {"py/tuple": []}, null, null, {"py/tuple": [{"py/tuple": ["Trigger", {"callback": null, "type": {"py/type": "builtins.str"}}]}, {"py/tuple": ["awsdir", {"callback": null, "type": {"py/type": "builtins.str"}}]}, {"py/tuple": ["bucket", {"callback": null, "type": {"py/type": "builtins.str"}}]}, {"py/tuple": ["downloadDir", {"callback": null, "type": {"py/type": "builtins.str"}}]}]}]}, "outputs": {"py/reduce": [{"py/type": "collections.OrderedDict"}, {"py/tuple": []}, null, null, {"py/tuple": [{"py/tuple": ["downloadDir", {"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": ["awsdir", {"default": "/data/.aws", "flag": null, "argument": true, "label": "AWS directory", "type": "directory"}]}, {"py/tuple": ["bucket", {"default": "myBucket", "flag": null, "argument": true, "label": "S3 bucket", "type": "str"}]}, {"py/tuple": ["downloadDir", {"default": "/data", "flag": null, "argument": true, "label": "Directory to download to", "type": "directory"}]}, {"py/tuple": ["dirs", {"flag": null, "label": "S3 objects to download", "type": "text list", "env": "DIRS"}]}, {"py/tuple": ["nthreads", {"flag": null, "label": "Number of Threads", "type": "int", "env": "nThreads"}]}, {"py/tuple": ["key", {"flag": null, "label": "AWS Access key", "type": "str", "env": "AWS_ACCESS_KEY_ID"}]}, {"py/tuple": ["secret", {"flag": null, "label": "AWS Secret", "type": "str", "env": "AWS_SECRET_ACCESS_KEY"}]}, {"py/tuple": ["region", {"default": "us-east-2", "flag": null, "label": "Region", "type": "str", "env": "AWS_DEFAULT_REGION"}]}]}]}, "command": ["download.sh"], "autoMap": true, "runDockerMap": null, "persistentSettings": "all", "requiredParameters": ["awsdir", "bucket", "downloadDir", "dirs"]}
diff --git a/nfcore_star_salmon/widgets/nfcore_star_salmon/S3_download/S3_download.py b/nfcore_star_salmon/widgets/nfcore_star_salmon/S3_download/S3_download.py
@@ -0,0 +1,71 @@
+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 OWS3_download(OWBwBWidget):
+    name = "S3_download"
+    description = "Enter and output a file"
+    priority = 10
+    icon = getIconName(__file__,"downloadS3.png")
+    want_main_area = False
+    docker_image_name = "biodepot/s3download"
+    docker_image_tag = "1.16.272__python_3.8.0__alpine-3.10__e2962454"
+    inputs = [("Trigger",str,"handleInputsTrigger"),("awsdir",str,"handleInputsawsdir"),("bucket",str,"handleInputsbucket"),("downloadDir",str,"handleInputsdownloadDir")]
+    outputs = [("downloadDir",str)]
+    pset=functools.partial(settings.Setting,schema_only=True)
+    runMode=pset(0)
+    exportGraphics=pset(False)
+    runTriggers=pset([])
+    triggerReady=pset({})
+    inputConnectionsStore=pset({})
+    optionsChecked=pset({})
+    awsdir=pset("/data/.aws")
+    bucket=pset("myBucket")
+    downloadDir=pset("/data")
+    dirs=pset([])
+    nthreads=pset(None)
+    key=pset(None)
+    secret=pset(None)
+    region=pset("us-east-2")
+    def __init__(self):
+        super().__init__(self.docker_image_name, self.docker_image_tag)
+        with open(getJsonName(__file__,"S3_download")) as f:
+            self.data=jsonpickle.decode(f.read())
+            f.close()
+        self.initVolumes()
+        self.inputConnections = ConnectionDict(self.inputConnectionsStore)
+        self.drawGUI()
+    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 handleInputsawsdir(self, value, *args):
+        if args and len(args) > 0: 
+            self.handleInputs("awsdir", value, args[0][0], test=args[0][3])
+        else:
+            self.handleInputs("inputFile", value, None, False)
+    def handleInputsbucket(self, value, *args):
+        if args and len(args) > 0: 
+            self.handleInputs("bucket", value, args[0][0], test=args[0][3])
+        else:
+            self.handleInputs("inputFile", value, None, False)
+    def handleInputsdownloadDir(self, value, *args):
+        if args and len(args) > 0: 
+            self.handleInputs("downloadDir", value, args[0][0], test=args[0][3])
+        else:
+            self.handleInputs("inputFile", value, None, False)
+    def handleOutputs(self):
+        outputValue=None
+        if hasattr(self,"downloadDir"):
+            outputValue=getattr(self,"downloadDir")
+        self.send("downloadDir", outputValue)