Unable to pass path to refen

[AMCalejandro]

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