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Fixed relative path issue #65 and modified example workflows and Agav…
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…e system data.sciapps.org
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Liya Wang committed Mar 6, 2017
1 parent 77f77b1 commit 657702a
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2 changes: 1 addition & 1 deletion agavedancer/public/assets/Annotation.workflow.json
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{"id":"e2d822fc-8076-4f9e-8487-48d0b328d7e9","name":"Annotation.workflow","description":"","steps":[{"id":0,"appId":"MAKER-0.0.1","jobId":"5901933915690701286-242ac115-0001-007","inputs":{"protein":"agave://data.sciapps.org/maker/msu-irgsp-proteins.fasta","est":"agave://data.sciapps.org/maker/mRNA.fasta","repeat":"agave://data.sciapps.org/maker/plant_repeats.fasta","genome":"agave://data.sciapps.org/maker/test_genome.fasta"},"parameters":{"always_complete":null,"pred_flank":200,"split_hit":10000,"min_contig":1,"max_dna_len":100000,"correct_est_fusion":null,"alt_splice":null}},{"id":1,"appId":"SNAP-0.0.1","jobId":"7088983986346332646-242ac115-0001-007","inputs":{"gff":{"step":0,"output_name":"my.all.gff.gz"}},"parameters":{"intg":1000}},{"id":2,"appId":"MAKER-0.0.1","jobId":"3929012853509778970-242ac115-0001-007","inputs":{"otherEvidences":{"step":0,"output_name":"my.all.gff.gz"},"hmm":{"step":1,"output_name":"my.all.hmm"},"genome":"agave://data.sciapps.org/maker/test_genome.fasta"},"parameters":{"always_complete":null,"pred_flank":200,"split_hit":10000,"min_contig":1,"max_dna_len":100000,"correct_est_fusion":null,"alt_splice":null}},{"id":3,"appId":"SNAP-0.0.1","jobId":"3801440711226945050-242ac115-0001-007","inputs":{"gff":{"step":2,"output_name":"my.all.gff.gz"}},"parameters":{"intg":1000}},{"id":4,"appId":"MAKER-0.0.1","jobId":"3285427125864960486-242ac115-0001-007","inputs":{"otherEvidences":{"step":2,"output_name":"my.all.gff.gz"},"hmm":{"step":3,"output_name":"my.all.hmm"},"genome":"agave://data.sciapps.org/maker/test_genome.fasta"},"parameters":{"always_complete":null,"pred_flank":200,"split_hit":10000,"min_contig":1,"max_dna_len":100000,"correct_est_fusion":null,"alt_splice":null}}]}
{"id":"e2d822fc-8076-4f9e-8487-48d0b328d7e9","name":"Annotation.workflow","description":"","steps":[{"id":0,"appId":"MAKER-0.0.1","jobId":"5901933915690701286-242ac115-0001-007","inputs":{"protein":"agave://data.sciapps.org/example_data/maker/msu-irgsp-proteins.fasta","est":"agave://data.sciapps.org/example_data/maker/mRNA.fasta","repeat":"agave://data.sciapps.org/example_data/maker/plant_repeats.fasta","genome":"agave://data.sciapps.org/example_data/maker/test_genome.fasta"},"parameters":{"always_complete":null,"pred_flank":200,"split_hit":10000,"min_contig":1,"max_dna_len":100000,"correct_est_fusion":null,"alt_splice":null}},{"id":1,"appId":"SNAP-0.0.1","jobId":"7088983986346332646-242ac115-0001-007","inputs":{"gff":{"step":0,"output_name":"my.all.gff.gz"}},"parameters":{"intg":1000}},{"id":2,"appId":"MAKER-0.0.1","jobId":"3929012853509778970-242ac115-0001-007","inputs":{"otherEvidences":{"step":0,"output_name":"my.all.gff.gz"},"hmm":{"step":1,"output_name":"my.all.hmm"},"genome":"agave://data.sciapps.org/example_data/maker/test_genome.fasta"},"parameters":{"always_complete":null,"pred_flank":200,"split_hit":10000,"min_contig":1,"max_dna_len":100000,"correct_est_fusion":null,"alt_splice":null}},{"id":3,"appId":"SNAP-0.0.1","jobId":"3801440711226945050-242ac115-0001-007","inputs":{"gff":{"step":2,"output_name":"my.all.gff.gz"}},"parameters":{"intg":1000}},{"id":4,"appId":"MAKER-0.0.1","jobId":"3285427125864960486-242ac115-0001-007","inputs":{"otherEvidences":{"step":2,"output_name":"my.all.gff.gz"},"hmm":{"step":3,"output_name":"my.all.hmm"},"genome":"agave://data.sciapps.org/example_data/maker/test_genome.fasta"},"parameters":{"always_complete":null,"pred_flank":200,"split_hit":10000,"min_contig":1,"max_dna_len":100000,"correct_est_fusion":null,"alt_splice":null}}]}
2 changes: 1 addition & 1 deletion agavedancer/public/assets/Association.workflow.json
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{"id":"be58ead0-6c45-43a2-b54b-8fdda947e4b9","name":"Association.workflow","description":"","steps":[{"id":0,"appId":"ConvertTraitID-0.0.0","jobId":"7541259367061197286-242ac115-0001-007","inputs":{"trait":"agave://data.sciapps.org/gwas_raw/height.txt"},"parameters":{"sid":"Sorghum","header":0}},{"id":1,"appId":"MergeG2P-0.0.2","jobId":"7083916814911532570-242ac115-0001-007","inputs":{"sid":"agave://data.sciapps.org/gwas_raw/myStudy_filt.c9.hmp.txt","trait":{"step":0,"output_name":"tnrs.txt"}},"parameters":{"headlines":1,"extracols":11}},{"id":2,"appId":"NPUTE-0.0.1","jobId":"7274773547954138650-242ac115-0001-007","inputs":{"i":{"step":1,"output_name":"m_marker.txt"}},"parameters":{"stepWindow":1,"endWindow":5,"mode":"Imputing","missing":"N","startWindow":2,"ploidy":"1","extracols":11,"header":1}},{"id":3,"appId":"NumericalTransform-TASSEL-4.3.15","jobId":"1863831980171062810-242ac115-0001-007","inputs":{"h":{"step":2,"output_name":"imputed.txt"}},"parameters":{"numericalGenoTransform":"collapse","markerformat":"Hapmap","minfreq":"0.05"}},{"id":4,"appId":"CloudSTRUCTURE-2.3.4","jobId":"6431174488491748890-242ac115-0001-007","inputs":{"i":{"step":3,"output_name":"nt.txt"}},"parameters":{"numinds":310,"phaseinfo":false,"burnin":1000,"mapdistances":false,"missing":"-9","numloci":12098,"popdata":false,"maxpops":3,"numreps":1000,"markernames":true,"popflag":false,"onerowperind":true,"phenotype":false,"ploidy":1,"label":true,"markovphase":false,"extracols":0}},{"id":5,"appId":"MLM-TASSEL-5.1.23","jobId":"3893938504683950566-242ac115-0001-007","inputs":{"rtrait":{"step":1,"output_name":"m_trait.txt"},"qstructure":{"step":4,"output_name":"s3_f"},"hmarker":{"step":2,"output_name":"imputed.txt"}},"parameters":{"level":1,"mlmVarCompEst":"P3D","filter":"0.05","markerformat":"Hapmap","maxp":1,"mlmCompressionLevel":"Optimum"}},{"id":6,"appId":"XYPlot-0.0.2","jobId":"3384438147951104486-242ac115-0001-007","inputs":{"i":{"step":5,"output_name":"MLM2.txt"}},"parameters":{"xlabel":"Loci","ycol":7,"ylabel":"-log(Pval)","type":false,"logt":true,"title":"MLM","xcol":4}}]}
{"id":"be58ead0-6c45-43a2-b54b-8fdda947e4b9","name":"Association.workflow","description":"","steps":[{"id":0,"appId":"ConvertTraitID-0.0.0","jobId":"7541259367061197286-242ac115-0001-007","inputs":{"trait":"agave://data.sciapps.org/example_data/gwas_raw/height.txt"},"parameters":{"sid":"Sorghum","header":0}},{"id":1,"appId":"MergeG2P-0.0.2","jobId":"7083916814911532570-242ac115-0001-007","inputs":{"sid":"agave://data.sciapps.org/example_data/gwas_raw/myStudy_filt.c9.hmp.txt","trait":{"step":0,"output_name":"tnrs.txt"}},"parameters":{"headlines":1,"extracols":11}},{"id":2,"appId":"NPUTE-0.0.1","jobId":"7274773547954138650-242ac115-0001-007","inputs":{"i":{"step":1,"output_name":"m_marker.txt"}},"parameters":{"stepWindow":1,"endWindow":5,"mode":"Imputing","missing":"N","startWindow":2,"ploidy":"1","extracols":11,"header":1}},{"id":3,"appId":"NumericalTransform-TASSEL-4.3.15","jobId":"1863831980171062810-242ac115-0001-007","inputs":{"h":{"step":2,"output_name":"imputed.txt"}},"parameters":{"numericalGenoTransform":"collapse","markerformat":"Hapmap","minfreq":"0.05"}},{"id":4,"appId":"CloudSTRUCTURE-2.3.4","jobId":"6431174488491748890-242ac115-0001-007","inputs":{"i":{"step":3,"output_name":"nt.txt"}},"parameters":{"numinds":310,"phaseinfo":false,"burnin":1000,"mapdistances":false,"missing":"-9","numloci":12098,"popdata":false,"maxpops":3,"numreps":1000,"markernames":true,"popflag":false,"onerowperind":true,"phenotype":false,"ploidy":1,"label":true,"markovphase":false,"extracols":0}},{"id":5,"appId":"MLM-TASSEL-5.1.23","jobId":"3893938504683950566-242ac115-0001-007","inputs":{"rtrait":{"step":1,"output_name":"m_trait.txt"},"qstructure":{"step":4,"output_name":"s3_f"},"hmarker":{"step":2,"output_name":"imputed.txt"}},"parameters":{"level":1,"mlmVarCompEst":"P3D","filter":"0.05","markerformat":"Hapmap","maxp":1,"mlmCompressionLevel":"Optimum"}},{"id":6,"appId":"XYPlot-0.0.2","jobId":"3384438147951104486-242ac115-0001-007","inputs":{"i":{"step":5,"output_name":"MLM2.txt"}},"parameters":{"xlabel":"Loci","ycol":7,"ylabel":"-log(Pval)","type":false,"logt":true,"title":"MLM","xcol":4}}]}
2 changes: 1 addition & 1 deletion agavedancer/public/javascripts/components/appsInput.js
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Expand Up @@ -30,7 +30,7 @@ const AppsInput=React.createClass({

handleDsStoreChange: function(dsStore) {
let dsItemPath=dsStore.dsItemPaths[this.props.data.id];
let dsItemUrl=dsItemPath ? 'agave://' + this.state.setting.datastore_system + '/' + dsItemPath : '';
let dsItemUrl=dsItemPath ? 'agave://' + this.state.setting.datastore_system + '/example_data/' + dsItemPath : '';
if (dsItemUrl && dsItemUrl !== this.state.textValue) {
this.setState({
textValue: dsItemUrl
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2 changes: 1 addition & 1 deletion agavedancer/public/javascripts/components/filesInfo.js
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Expand Up @@ -23,7 +23,7 @@ const FilesInfo=React.createClass({
);
});
let fileName=fileDetail['path'].replace(/.*\// ,'');
let link='http://' + fileDetail['system'] + '/example_data/' + fileDetail['path'];
let link='http://' + fileDetail['system'] + '/' + fileDetail['path'];
tbody.push(<tr key={'source'}><th><a href={link} target="_blank">Link to File</a></th><td></td></tr>);
markup=(
<Table striped condensed hover>
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