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8.0 2.0 7.0 8.78 MB

License: Apache License 2.0

R 22.49% Dockerfile 1.48% Jupyter Notebook 76.03%
bioinformatics bioinformatics-tool bioinformatics-data bioinformatics-databases dbgap r rpackage dockerfile docker-image sratoolkit

dbgap2x's People

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gversmee avatar mik4unix avatar mikaeldusenne avatar

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dbgap2x's Issues

query search.dbgap("Jackson", no.browser = TRUE)

This function is important to the tool, but only returns the URL of the dbgap page listing the studies. Would prefer to return a structured summary of those studies, so that it can be used in combination with other queries.

Output format from parent.study function

Hi! I observed the weird format of output from parent.study() function.

parent.study("phs000090")
[1] " 'phs000280.v6.p1" ""

(space) ' in the first element and the empty string in the second element.
Do you know why I got this? Thanks.

> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.3

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] dbgap2x_1.0 dplyr_0.8.5

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3        pillar_1.4.3      compiler_3.6.2    bitops_1.0-6      prettyunits_1.1.1 remotes_2.1.1    
 [7] tools_3.6.2       testthat_2.3.2    digest_0.6.25     pkgbuild_1.0.6    pkgload_1.0.2     jsonlite_1.6.1   
[13] memoise_1.1.0     tibble_2.1.3      pkgconfig_2.0.3   rlang_0.4.5       cli_2.0.2         parallel_3.6.2   
[19] curl_4.3          yaml_2.2.1        xfun_0.12         httr_1.4.1        withr_2.1.2       stringr_1.4.0    
[25] knitr_1.28        vctrs_0.2.4       desc_1.2.0        fs_1.3.2          devtools_2.2.2    rprojroot_1.3-2  
[31] tidyselect_1.0.0  data.table_1.12.8 glue_1.3.1        R6_2.4.1          processx_3.4.2    fansi_0.4.1      
[37] XML_3.99-0.3      sessioninfo_1.1.1 callr_3.4.2       purrr_0.3.3       magrittr_1.5      backports_1.1.5  
[43] ps_1.3.2          ellipsis_0.3.0    usethis_1.5.1     assertthat_0.2.1  utf8_1.1.4        stringi_1.4.6    
[49] RCurl_1.98-1.1    crayon_1.3.4  

Size of Docker image

10Gb is way too much
The Docker image took 40 min to download, and after checking, docker image is 10Gb. My understanding is that dbGaP2x only requires a jupyter server, a few dev libraries and a R environment. The image should be much less than 1Gb.

Error in parallel::mclapply

Hi Authors!!

I am trying to use this package. When I run the exemplary command in R i.e. search.dbgap("Jackson") it throws the following error:

Error in parallel::mclapply(mc.cores = getOption("mc.cores", parallel::detectCores()),  : 
  'mc.cores' > 1 is not supported on Windows

Please help me understand how to deal with this?

htmlTable

It looks like htmlTable package needs to be manually installed before installing the package via devtools

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