From e997f3111e57a6016faff67b9d362018678b0162 Mon Sep 17 00:00:00 2001 From: js2264 Date: Mon, 22 Jan 2024 13:01:30 +0100 Subject: [PATCH] fix: skip fourDNData pairs parsing for now (2) --- Dockerfile | 2 +- inst/pages/disseminating.qmd | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index 33a1bb9..f49a7c9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,7 +3,7 @@ FROM bioconductor/bioconductor_docker:${BIOC_VERSION} COPY . /opt/pkg # Install book package -RUN Rscript -e 'repos <- BiocManager::repositories() ; remotes::install_github("lawremi/rtracklayer") ; remotes::install_local(path = "/opt/pkg/", repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE) ; sessioninfo::session_info(installed.packages()[,"Package"], include_base = TRUE)' +RUN Rscript -e 'repos <- BiocManager::repositories() ; remotes::install_github("lawremi/rtracklayer") ; remotes::install_github("js2264/HiContactsData") ; remotes::install_local(path = "/opt/pkg/", repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE) ; sessioninfo::session_info(installed.packages()[,"Package"], include_base = TRUE)' ## Build/install using same approach than BBS RUN R CMD INSTALL /opt/pkg diff --git a/inst/pages/disseminating.qmd b/inst/pages/disseminating.qmd index aeaa2a4..c0b507d 100644 --- a/inst/pages/disseminating.qmd +++ b/inst/pages/disseminating.qmd @@ -86,7 +86,8 @@ type of file to fetch can be specified with the `type` argument: - `type = 'pairs'` will fetch the pairs file which was generated by the 4DN consortium and binned into a contact matrix. Once fetched from the 4DN data portal, the local file can be imported in `R` using the `import` function, which will generate a `GInteractions` object. -```{r} +```{r eval = FALSE} +## Not evaluated for now pairs_f <- fourDNData(experimentSetAccession = '4DNESJNPEKZD', type = 'pairs') print(pairs_f) import(pairs_f) @@ -102,8 +103,7 @@ a large storage footprint. - `type = 'insulation'` will fetch a `.bigwig` track file precomputed by the 4DN consortium. This track corresponds to the genome-wide insulation score computed by `cooltools` as described in @Crane_2015. To know more about this, read [the excerpt from 4DN data portal](https://data.4dnucleome.org/resources/data-analysis/insulation_compartment_scores#insulation_scores_and_boundaries_page_all). Once fetched from the 4DN data portal, the local file can be imported in `R` using the `import` function, which will generate a `RleList` object. -```{r eval = FALSE} -## Not evaluated for now +```{r} library(rtracklayer) fourDNData(experimentSetAccession = '4DNES25ABNZ1', type = 'insulation') |> import(as = 'Rle')