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neurogenomics / MAGMA_Celltyping

Find causal cell-types underlying complex trait genetics
https://neurogenomics.github.io/MAGMA_Celltyping
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Unable to pass path to refen #124

Open AMCalejandro opened 1 year ago

AMCalejandro commented 1 year ago

1. Bug description

I cant specify I have my reference panel locally

Code and console output

> pdrisk_genesout <- MAGMA.Celltyping::map_snps_to_genes(
+     path_formatted = "/home/rstudio/cellType_progGWAS/data/pd_gwas/qc_gwas/pdriskGWAS_ldscQCed.tsv",
+     upstream_kb = 35,
+     downstream_kb = 10,
+     genome_build = "GRCh37",
+     N = round(mean(pdrisk$N)),
+     population = "eur",
+     #storage_dir = "~/cellType_progGWAS/workflow/magma_celltyping/")
+     #genome_ref_path = "~/software/magma_software/reference_data/g1000_eur"
+     genome_ref_path = "~/software/magma_software/reference_data/")
Installed MAGMA version: v1.10
Skipping MAGMA installation.
The desired_version of MAGMA is currently installed: v1.10
Using: magma_v1.10
genome_ref not found in storage_dir. Downloading from remote server instead ==> /home/rstudio/software/magma_software
trying URL 'https://ctg.cncr.nl/software/MAGMA/ref_data/magma_software.zip'
Error in utils::download.file(url = input_url, destfile = zipfile) : 
  cannot open URL 'https://ctg.cncr.nl/software/MAGMA/ref_data/magma_software.zip'
In addition: Warning message:
In utils::download.file(url = input_url, destfile = zipfile) :
  cannot open URL 'https://ctg.cncr.nl/software/MAGMA/ref_data/magma_software.zip': HTTP status was '404 Not Found'
> 
> pdrisk_genesout <- MAGMA.Celltyping::map_snps_to_genes(
+     path_formatted = "/home/rstudio/cellType_progGWAS/data/pd_gwas/qc_gwas/pdriskGWAS_ldscQCed.tsv",
+     upstream_kb = 35,
+     downstream_kb = 10,
+     genome_build = "GRCh37",
+     N = round(mean(pdrisk$N)),
+     population = "eur",
+     #storage_dir = "~/cellType_progGWAS/workflow/magma_celltyping/")
+     #genome_ref_path = "~/software/magma_software/reference_data/g1000_eur"
+     genome_ref_path = "~/software/magma_software/reference_data/g1000_eur/")
Installed MAGMA version: v1.10
Skipping MAGMA installation.
The desired_version of MAGMA is currently installed: v1.10
Using: magma_v1.10
genome_ref not found in storage_dir. Downloading from remote server instead ==> /home/rstudio/software/magma_software/reference_data
trying URL 'https://ctg.cncr.nl/software/MAGMA/ref_data/reference_data.zip'
Error in utils::download.file(url = input_url, destfile = zipfile) : 
  cannot open URL 'https://ctg.cncr.nl/software/MAGMA/ref_data/reference_data.zip'
In addition: Warning message:
In utils::download.file(url = input_url, destfile = zipfile) :
  cannot open URL 'https://ctg.cncr.nl/software/MAGMA/ref_data/reference_data.zip': HTTP status was '404 Not Found'

Data

I am pasting here the directory I am pointing out with genome_ref_path

rstudio@3e36fec3eec9:~/software/magma_software/reference_data$ ls
g1000_eur  README

rstudio@3e36fec3eec9:~/software/magma_software/reference_data$ ls g1000_eur/
g1000_eur.bed  g1000_eur.bim  g1000_eur.fam  g1000_eur.synonyms  g1000_eur.zip

3. Session info

``` > sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.5 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] data.table_1.14.2 MAGMA.Celltyping_2.0.7 forcats_0.5.2 stringr_1.4.1 dplyr_1.0.10 purrr_0.3.4 [7] readr_2.1.2 tidyr_1.2.0 tibble_3.1.8 ggplot2_3.3.6 tidyverse_1.3.2 here_1.0.1 loaded via a namespace (and not attached): [1] utf8_1.2.2 R.utils_2.12.0 tidyselect_1.1.2 lme4_1.1-30 RSQLite_2.2.16 [6] AnnotationDbi_1.59.1 htmlwidgets_1.5.4 grid_4.2.0 BiocParallel_1.31.12 munsell_0.5.0 [11] codetools_0.2-18 withr_2.5.0 colorspace_2.0-3 Biobase_2.57.1 filelock_1.0.2 [16] knitr_1.40 rstudioapi_0.14 orthogene_1.3.2 stats4_4.2.0 SingleCellExperiment_1.19.0 [21] ggsignif_0.6.3 MatrixGenerics_1.9.1 GenomeInfoDbData_1.2.8 bit64_4.0.5 rprojroot_2.0.3 [26] vctrs_0.4.1 treeio_1.21.2 generics_0.1.3 xfun_0.32 BiocFileCache_2.5.0 [31] R6_2.5.1 GenomeInfoDb_1.33.5 bitops_1.0-7 cachem_1.0.6 gridGraphics_0.5-1 [36] DelayedArray_0.23.1 assertthat_0.2.1 promises_1.2.0.1 BiocIO_1.7.1 scales_1.2.1 [41] googlesheets4_1.0.1 gtable_0.3.1 rlang_1.0.5 MungeSumstats_1.5.13 splines_4.2.0 [46] rtracklayer_1.57.0 rstatix_0.7.0 lazyeval_0.2.2 gargle_1.2.0 broom_1.0.1 [51] BiocManager_1.30.18 yaml_2.3.5 reshape2_1.4.4 abind_1.4-5 modelr_0.1.9 [56] GenomicFeatures_1.49.6 backports_1.4.1 httpuv_1.6.5 tools_4.2.0 ggplotify_0.1.0 [61] ellipsis_0.3.2 ggdendro_0.1.23 BiocGenerics_0.43.1 Rcpp_1.0.9 plyr_1.8.7 [66] progress_1.2.2 zlibbioc_1.43.0 RCurl_1.98-1.8 prettyunits_1.1.1 ggpubr_0.4.0 [71] S4Vectors_0.35.3 SummarizedExperiment_1.27.2 haven_2.5.1 fs_1.5.2 magrittr_2.0.3 [76] reprex_2.0.2 googledrive_2.0.0 matrixStats_0.62.0 hms_1.1.2 patchwork_1.1.2 [81] mime_0.12 xtable_1.8-4 XML_3.99-0.10 EWCE_1.5.7 readxl_1.4.1 [86] IRanges_2.31.2 gridExtra_2.3 compiler_4.2.0 biomaRt_2.53.2 crayon_1.5.1 [91] minqa_1.2.4 R.oo_1.25.0 htmltools_0.5.3 ggfun_0.0.7 later_1.3.0 [96] tzdb_0.3.0 aplot_0.1.6 lubridate_1.8.0 DBI_1.1.3 ExperimentHub_2.5.0 [101] gprofiler2_0.2.1 dbplyr_2.2.1 MASS_7.3-58.1 rappdirs_0.3.3 boot_1.3-28 [106] babelgene_22.3 Matrix_1.4-1 car_3.1-0 cli_3.3.0 R.methodsS3_1.8.2 [111] parallel_4.2.0 GenomicRanges_1.49.1 pkgconfig_2.0.3 GenomicAlignments_1.33.1 plotly_4.10.0 [116] xml2_1.3.3 ggtree_3.5.3 XVector_0.37.1 rvest_1.0.3 yulab.utils_0.0.5 [121] VariantAnnotation_1.43.3 digest_0.6.29 Biostrings_2.65.3 cellranger_1.1.0 HGNChelper_0.8.1 [126] tidytree_0.4.0 restfulr_0.0.15 curl_4.3.2 shiny_1.7.2 Rsamtools_2.13.4 [131] rjson_0.2.21 nloptr_2.0.3 lifecycle_1.0.1 nlme_3.1-159 jsonlite_1.8.0 [136] carData_3.0-5 viridisLite_0.4.1 limma_3.53.6 BSgenome_1.65.2 fansi_1.0.3 [141] pillar_1.8.1 lattice_0.20-45 homologene_1.4.68.19.3.27 KEGGREST_1.37.3 fastmap_1.1.0 [146] httr_1.4.4 googleAuthR_2.0.0 interactiveDisplayBase_1.35.0 glue_1.6.2 RNOmni_1.0.1 [151] png_0.1-7 ewceData_1.5.0 BiocVersion_3.16.0 bit_4.0.4 stringi_1.7.8 [156] blob_1.2.3 AnnotationHub_3.5.0 memoise_2.0.1 ape_5.6-2 ```