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ls\n",{"type":430,"tag":590,"props":742,"children":744},{"class":592,"line":743},3,[745],{"type":430,"tag":590,"props":746,"children":748},{"emptyLinePlaceholder":747},true,[749],{"type":435,"value":750},"\n",{"type":430,"tag":590,"props":752,"children":754},{"class":592,"line":753},4,[755],{"type":430,"tag":590,"props":756,"children":757},{"style":618},[758],{"type":435,"value":759},"# list all available files for the tool\n",{"type":430,"tag":590,"props":761,"children":763},{"class":592,"line":762},5,[764,768,773],{"type":430,"tag":590,"props":765,"children":766},{"style":597},[767],{"type":435,"value":600},{"type":430,"tag":590,"props":769,"children":770},{"style":603},[771],{"type":435,"value":772}," find",{"type":430,"tag":590,"props":774,"children":775},{"style":603},[776],{"type":435,"value":777}," .\n",{"type":430,"tag":590,"props":779,"children":781},{"class":592,"line":780},6,[782],{"type":430,"tag":590,"props":783,"children":784},{"emptyLinePlaceholder":747},[785],{"type":435,"value":750},{"type":430,"tag":590,"props":787,"children":789},{"class":592,"line":788},7,[790],{"type":430,"tag":590,"props":791,"children":792},{"style":618},[793],{"type":435,"value":794},"# list all commands\n",{"type":430,"tag":590,"props":796,"children":798},{"class":592,"line":797},8,[799,803],{"type":430,"tag":590,"props":800,"children":801},{"style":597},[802],{"type":435,"value":600},{"type":430,"tag":590,"props":804,"children":805},{"style":603},[806],{"type":435,"value":807}," --help\n",{"type":430,"tag":449,"props":809,"children":811},{"id":810},"uploading-data",[812],{"type":435,"value":813},"Uploading data",{"type":430,"tag":431,"props":815,"children":816},{},[817],{"type":435,"value":818},"You can use the following process to upload data to be used by St. Jude Cloud Platform tools:",{"type":430,"tag":509,"props":820,"children":821},{},[822,836,849,862],{"type":430,"tag":513,"props":823,"children":824},{},[825,827,834],{"type":435,"value":826},"First, click \"View\" on the tool you'd like to run from ",{"type":430,"tag":438,"props":828,"children":831},{"href":829,"rel":830},"https://platform.stjude.cloud/workflows",[442],[832],{"type":435,"value":833},"this page",{"type":435,"value":835},".\nIn this example, we will choose the Rapid RNA-Seq tool.",{"type":430,"tag":513,"props":837,"children":838},{},[839,841,844],{"type":435,"value":840},"If you have not already, click \"Start\" on the tool you'd like to run.\nThis will create a cloud workspace for you to upload your data to with the same name as the tool.",{"type":430,"tag":503,"props":842,"children":843},{},[],{"type":430,"tag":686,"props":845,"children":848},{"alt":846,"src":847},"rapid rna seq start page","/img/genomics-platform/analyzing-data/command-line-interaction/RapidRNASeq_startPage.png",[],{"type":430,"tag":513,"props":850,"children":851},{},[852,854,857],{"type":435,"value":853},"Open up your terminal application and select the cloud workspace with the same name as the tool you are trying to run.",{"type":430,"tag":503,"props":855,"children":856},{},[],{"type":430,"tag":686,"props":858,"children":861},{"alt":859,"src":860},"select rapid rna seq","/img/genomics-platform/analyzing-data/command-line-interaction/select-rapid-rnaseq.png",[],{"type":430,"tag":513,"props":863,"children":864},{},[865,867,873,875,881,883,886],{"type":435,"value":866},"Last, navigate to the local files you'd like to upload to the cloud and use the ",{"type":430,"tag":541,"props":868,"children":870},{"className":869},[],[871],{"type":435,"value":872},"dx upload",{"type":435,"value":874}," command as specified in ",{"type":430,"tag":590,"props":876,"children":878},{"role":877},"ref",[879],{"type":435,"value":880},"upload-download-data",{"type":435,"value":882}," to upload your data to St. Jude Cloud.",{"type":430,"tag":503,"props":884,"children":885},{},[],{"type":430,"tag":686,"props":887,"children":890},{"alt":888,"src":889},"rna seq upload","/img/genomics-platform/analyzing-data/command-line-interaction/rapid-rnaseq-upload-data.png",[],{"type":430,"tag":449,"props":892,"children":894},{"id":893},"downloading-data",[895],{"type":435,"value":896},"Downloading data",{"type":430,"tag":488,"props":898,"children":901},{"color":899,"icon":900},"orange","i-heroicons-exclamation-circle",[902],{"type":430,"tag":431,"props":903,"children":904},{},[905,910,913],{"type":430,"tag":497,"props":906,"children":907},{},[908],{"type":435,"value":909},"Warning",{"type":430,"tag":503,"props":911,"children":912},{},[],{"type":435,"value":914},"\nTo download data from a St. Jude Cloud data request, you must have indicated that you wished to download the data in your Data Access Agreement (DAA) during your submission.\nAny downloading of St. Jude data without completing this step is strictly PROHIBITED.",{"type":430,"tag":431,"props":916,"children":917},{},[918],{"type":435,"value":919},"You can use the following steps to download data from a St. Jude Cloud data request:",{"type":430,"tag":509,"props":921,"children":922},{},[923,935,955,1006,1019],{"type":430,"tag":513,"props":924,"children":925},{},[926,928,933],{"type":435,"value":927},"Complete a data request using the Genomics Platform application.\nSee this ",{"type":430,"tag":438,"props":929,"children":930},{"href":40},[931],{"type":435,"value":932},"guide",{"type":435,"value":934}," for instructions.",{"type":430,"tag":513,"props":936,"children":937},{},[938,940,946,947,950],{"type":435,"value":939},"Open up your terminal application and select the cloud workspace relevant to your data request.\nFor instance, in this case we would type ",{"type":430,"tag":541,"props":941,"children":943},{"className":942},[],[944],{"type":435,"value":945},"#!bash dx select \"Retinoblastoma Data\"",{"type":435,"value":447},{"type":430,"tag":503,"props":948,"children":949},{},[],{"type":430,"tag":686,"props":951,"children":954},{"alt":952,"src":953},"select retinoblastoma","/img/genomics-platform/analyzing-data/command-line-interaction/select-retinoblastoma.png",[],{"type":430,"tag":513,"props":956,"children":957},{},[958,960,966,968,974,976,982,984,989,991,996,998,1001],{"type":435,"value":959},"You can use typical commands like ",{"type":430,"tag":541,"props":961,"children":963},{"className":962},[],[964],{"type":435,"value":965},"#!bash dx ls",{"type":435,"value":967},", ",{"type":430,"tag":541,"props":969,"children":971},{"className":970},[],[972],{"type":435,"value":973},"#!bash dx pwd",{"type":435,"value":975},", and ",{"type":430,"tag":541,"props":977,"children":979},{"className":978},[],[980],{"type":435,"value":981},"#!bash dx cd",{"type":435,"value":983}," to navigate around your cloud folder as you would a local folder.\nYour project may look different based on what data you requested and whether you were previously approved to access the data.\nYour data should either be in the ",{"type":430,"tag":497,"props":985,"children":986},{},[987],{"type":435,"value":988},"restricted",{"type":435,"value":990}," folder (if this is your first time requesting access) or the ",{"type":430,"tag":497,"props":992,"children":993},{},[994],{"type":435,"value":995},"immediate",{"type":435,"value":997}," folder (if you were previously granted access permission).",{"type":430,"tag":503,"props":999,"children":1000},{},[],{"type":430,"tag":686,"props":1002,"children":1005},{"alt":1003,"src":1004},"navigate data request","/img/genomics-platform/analyzing-data/command-line-interaction/navigate-data-request.png",[],{"type":430,"tag":513,"props":1007,"children":1008},{},[1009,1011,1017],{"type":435,"value":1010},"In the root of every data request is a file called ",{"type":430,"tag":541,"props":1012,"children":1014},{"className":1013},[],[1015],{"type":435,"value":1016},"SAMPLE_INFO.txt",{"type":435,"value":1018},".\nThis should contain all of the information about the samples you checked out as well as the associated metadata we provide.",{"type":430,"tag":513,"props":1020,"children":1021},{},[1022,1024,1030,1031,1035,1037,1043,1044,1047],{"type":435,"value":1023},"To download data from the cloud to local storage, use the ",{"type":430,"tag":541,"props":1025,"children":1027},{"className":1026},[],[1028],{"type":435,"value":1029},"#!bash dx download",{"type":435,"value":874},{"type":430,"tag":590,"props":1032,"children":1033},{"role":877},[1034],{"type":435,"value":880},{"type":435,"value":1036},".\nFor instance, if I wanted to download all of the BAM files to my local computer, I would type ",{"type":430,"tag":541,"props":1038,"children":1040},{"className":1039},[],[1041],{"type":435,"value":1042},"#!bash dx download immediate/bam/*",{"type":435,"value":447},{"type":430,"tag":503,"props":1045,"children":1046},{},[],{"type":430,"tag":686,"props":1048,"children":1051},{"alt":1049,"src":1050},"download bams","/img/genomics-platform/analyzing-data/command-line-interaction/download-bams.png",[],{"type":430,"tag":449,"props":1053,"children":1055},{"id":1054},"similar-topics",[1056],{"type":435,"value":1057},"Similar Topics",{"type":430,"tag":431,"props":1059,"children":1060},{},[1061,1066,1069,1073,1076,1081,1084],{"type":430,"tag":438,"props":1062,"children":1063},{"href":55},[1064],{"type":435,"value":1065},"About our Data",{"type":430,"tag":503,"props":1067,"children":1068},{},[],{"type":430,"tag":438,"props":1070,"children":1071},{"href":40},[1072],{"type":435,"value":39},{"type":430,"tag":503,"props":1074,"children":1075},{},[],{"type":430,"tag":438,"props":1077,"children":1078},{"href":67},[1079],{"type":435,"value":1080},"Working with our Data 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var(--shiki-dark-text-decoration);}",{"title":424,"searchDepth":614,"depth":614,"links":1096},[1097,1098,1099,1104,1105,1106],{"id":451,"depth":614,"text":5},{"id":461,"depth":614,"text":464},{"id":563,"depth":614,"text":566,"children":1100},[1101,1102,1103],{"id":570,"depth":743,"text":573},{"id":649,"depth":743,"text":652},{"id":693,"depth":743,"text":696},{"id":810,"depth":614,"text":813},{"id":893,"depth":614,"text":896},{"id":1054,"depth":614,"text":1057},"markdown","content:3.genomics-platform:4.analyzing-data:1.command-line-interaction.md","content","3.genomics-platform/4.analyzing-data/1.command-line-interaction.md","3.genomics-platform/4.analyzing-data/1.command-line-interaction","md",[1114,1116],{"_path":79,"title":1115,"description":424},"Filling Out The Extension Addendum",{"_path":89,"title":88,"description":1117},"In this guide, we will explain generally how to run, from end-to-end, any of our in house analysis workflows from within the DNAnexus cloud ecosystem.\nThe DNAnexus genomic ecosystem is the backbone for the computation and storage in St. Jude Cloud\nIf you'd like, you can read an introduction to the DNAnexus ecosystem here.\nIf you haven't already, follow this guide to request access to St. Jude data in this secure cloud ecosystem.",1791243637868]