Advanced tools and tutorials
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Polite inquiry about how to obtain the specific behavior pattern variables of accelerometry, such as the maximum daily sedentary bout length or the number of daily sedentary bouts?
- Former User of DNAx Community_75
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Issue stopping the dispensing option
- Former User of DNAx Community_6
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I am getting the following error when I try to run these lines in JupyterHub. Any help would be appreciated. sc = pyspark.SparkContext() spark = pyspark.sql.SparkSession(sc) RuntimeError: Java gateway process exited before sending its port number
- Former User of DNAx Community_11
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How to log all command outputs to the log file?
- Former User of DNAx Community_10
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How to view the job_error.json?
- Former User of DNAx Community_10
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ttyd vs. cloud station. What is the main difference?
- Former User of DNAx Community_20
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Issue running bolt lmm
- Former User of DNAx Community_6
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Different DNAnexus URLs
- Permanently deleted user
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CalledProcessError: Command '['/opt/notebooks/bgen.tgz/build/apps/bgenix', '-g', 'imputed/ukb21008_c1_b0_v1.bgen', '-incl-rsids', 'rs74045046']' returned non-zero exit status 255.
- Former User of DNAx Community_21
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index_bgen in RAP using imputation files
- Former User of DNAx Community_13
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I am creating a new workflow from scratch with my own custom apps. How can I have 1 central version of this workflow without needed to copy it to directories where the data is located? I want this workflow to be private to my project.
- Former User of DNAx Community_27
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Saige null model generation giving error when trying to do on the complete dataset
- Former User of DNAx Community_6
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Polite inquiry about how to efficiently analyze the huge raw data of accelerometry on RAP?
- Former User of DNAx Community_75
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Results of fewer SNPs total after using PJ Greer's scripts for Regenie using Plink genotype calls and final WES.
- Former User of DNAx Community_33
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When I create a notebook in JupyterLab from the DNAnexus tab (project storage), I can't open it. Message says its a protected project. Any suggestions? Do I have too always use dx download then?
- Former User of DNAx Community_97
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How to skip downloading files that already exist with dx download?
- Former User of DNAx Community_55
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Assistance with LMM-BOLT through the Swiss Army Knife platform: Assertion `CompressedSNPBlocks==1' failed.
- Former User of DNAx Community_25
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How can we set a retry policy on dx run jobs?
- Former User of DNAx Community_55
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Selection of the GFF file version
- Former User of DNAx Community_35
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Extract record tables using the dx command line.
- Former User of DNAx Community_60
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I having hard time using STATA 18 on Jupyter lab. Any suggestion on how I can do these ? Thank you
- Former User of DNAx Community_38
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How do I archive a folder? I know how to archive multiple files, but I want to archive all the files in one directory recursively.
- Former User of DNAx Community_100
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Extracting and saving a specific datafield for all participant in Jupyterlab,
- Former User of DNAx Community_59
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accessing the database through SQL Spark is not working
- Former User of DNAx Community_6
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WDL workflow and bash/R outputs in DNAnexus?
- Permanently deleted user
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Is it possible to run Snakemake pipelines on DNAnexus? I'm trying to use DROP () but having many issues running it, any previous code example on Snakemake that works on DNAnexus?
- Former User of DNAx Community_100
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Why does dx tools still have a Python2.7 dependency? Following the directions to install does not work because of this.
- Former User of DNAx Community_2
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What is the threshold value for Variant Allele Fraction and Reads on the Mutectcaller app?
- Permanently deleted user
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Can I filter when convert from BAM to VCF using the Mutectcaller app?
- Permanently deleted user
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Can we create our custom JupyterLab image and run it on DNANexus?
- Former User of DNAx Community_36
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