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"Repository", + "Repository": "CRAN", + "Hash": "0d0056cc5383fbc240ccd0cb584bf436" + } + } +} diff --git a/assets/report/report.qmd b/assets/report/report.qmd index dda84749..892854ba 100644 --- a/assets/report/report.qmd +++ b/assets/report/report.qmd @@ -20,7 +20,7 @@ css: logo.css --- ::: {.callout-note} -See the online [documentation](https://pgsc-calc.readthedocs.io/en/latest/output.html#report) for additional +See the online [documentation](https://pgsc-calc.readthedocs.io/en/latest/explanation/output.html) for additional explanation of the terms and data presented in this report. ::: @@ -383,7 +383,11 @@ melted_scores <- data.table::melt(scores, id.vars=id_cols, measure.vars=patterns # fixed in data.table 1.14.9 but not released yet score_names <- sub("_.*", "", colnames(scores)[grepl("_SUM$", colnames(scores))]) setattr(melted_scores$PGS, "levels", score_names) -data.table::fwrite(melted_scores, params$score_path, sep="\t", compress="gzip") + +# don't overwrite params$score_path until report has compiled +# OOM crashes can cause corrupted data +temp_out_path <- tempfile(fileext=".txt.gz") +data.table::fwrite(melted_scores, temp_out_path, sep="\t", compress="gzip") ``` ```{r, echo = FALSE, message = FALSE, eval=params$run_ancestry} @@ -504,3 +508,34 @@ For scores from the PGS Catalog, please remember to cite the original publicatio > PGS Catalog Calculator (in development). PGS Catalog Team. `https://github.com/PGScatalog/pgsc_calc` > Lambert et al. (2021) The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation. Nature Genetics. 53:420–425 doi:10.1038/s41588-021-00783-5. + +## Score licenses + +::: {.callout-tip} +* Scores deposited in the PGS Catalog may have specific license terms +* It's important to follow the license terms when you reuse scoring files +* Please check below for a summary of license terms +* License terms for custom scoring files aren't reported here, please check how the creators of the scoring file licensed their data +::: + +```{r} +# as of 2023-12-12 only non-default licenses are recorded in the scoring file header +default_ebi_terms <- "PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details." + +tibble::tibble(json = json_scorefiles) %>% + mutate(pgs_id = purrr::map_chr(json, ~ extract_chr_handle_null(.x, "pgs_id")), + license_text = purrr::map_chr(json, ~ extract_chr_handle_null(.x, "license"))) %>% + mutate(license_text = ifelse(license_text == "", default_ebi_terms, license_text)) %>% + # display license terms for files in the PGS Catalog only (with a PGS ID) + filter(startsWith(pgs_id, "PGS")) %>% + select(-json) %>% + DT::datatable(., colnames = c( + "PGS ID" = "pgs_id", + "License text" = "license_text" + )) +``` + +```{r cleanup, eval=!params$run_ancestry, echo=FALSE} +# prevent the report crashing from corrupting the aggregated scores +invisible(file.copy(temp_out_path, params$score_path, overwrite=TRUE)) +``` diff --git a/environments/report/Dockerfile b/environments/report/Dockerfile index 94693901..8d841a6d 100644 --- a/environments/report/Dockerfile +++ b/environments/report/Dockerfile @@ -1,6 +1,6 @@ ARG QUARTO_VERSION=1.3.433 -FROM r-base:4.3.0 +FROM continuumio/miniconda3 AS build ARG QUARTO_VERSION ARG TARGETARCH @@ -8,9 +8,18 @@ ARG TARGETARCH RUN wget https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-${TARGETARCH}.deb && \ dpkg -i quarto-${QUARTO_VERSION}-linux-${TARGETARCH}.deb && \ rm quarto-${QUARTO_VERSION}-linux-${TARGETARCH}.deb - -RUN R -e 'install.packages(c("DT", "data.table", "purrr", "jsonlite", "dplyr", "ggplot2", "tidyr", "forcats", "readr", "R.utils"), clean=TRUE)' + +RUN conda install -c conda-forge r-renv + +COPY renv.lock . + +ENV RENV_PATHS_LIBRARY renv/library + +RUN R -e "renv::restore(clean=TRUE, prompt=FALSE)" + +# RUN conda env export > environment.yml RUN apt-get update \ && apt-get install -y procps \ - && rm -rf /var/lib/apt/lists/* \ No newline at end of file + && rm -rf /var/lib/apt/lists/* +