diff --git a/.github/workflows/biocbook.yml b/.github/workflows/biocbook.yml index 99eea96..91bcd12 100644 --- a/.github/workflows/biocbook.yml +++ b/.github/workflows/biocbook.yml @@ -80,7 +80,7 @@ jobs: env: IMG: ${{ steps.docker.outputs.ImageID }} run: | - SHA=$(docker container create ${{ env.IMG }}) + SHA=$(docker container create ghcr.io/js2264/ohca:latest) docker container cp ${SHA}:/${{ env.Pkgname }}_${{ env.pkgversion }}.tar.gz . tar --extract --gzip --file ${{ env.Pkgname }}_${{ env.pkgversion }}.tar.gz echo bundle_path=${{ env.Pkgname }}_${{ env.pkgversion }}.tar.gz >> "${GITHUB_ENV}" diff --git a/inst/pages/workflow-chicken.qmd b/inst/pages/workflow-chicken.qmd index e67e728..43dc19f 100644 --- a/inst/pages/workflow-chicken.qmd +++ b/inst/pages/workflow-chicken.qmd @@ -64,7 +64,7 @@ samples <- list( '4DNESIR416OW' = 'prometaphase (15m)', '4DNESS8PTK6F' = 'prometaphase (30m)' ) -bpparam <- MulticoreParam(workers = 5, progressbar = TRUE) +bpparam <- MulticoreParam(workers = 5, progressbar = FALSE) hics <- bplapply(names(samples), fourDNHiCExperiment, BPPARAM = bpparam) ``` diff --git a/inst/pages/workflow-yeast.qmd b/inst/pages/workflow-yeast.qmd index 555e6ab..9a1f327 100644 --- a/inst/pages/workflow-yeast.qmd +++ b/inst/pages/workflow-yeast.qmd @@ -331,7 +331,7 @@ parallelization of independent correlation computation runs over multiple CPUs. ```{r eval = FALSE} # Some chromosomes will be ignored as they are too small for this analysis chrs <- c('II', 'IV', 'V', 'VII', 'VIII', 'IX', 'X', 'XI', 'XIII', 'XIV', 'XVI') -bpparam <- BiocParallel::MulticoreParam(workers = 6, progressbar = TRUE) +bpparam <- BiocParallel::MulticoreParam(workers = 6, progressbar = FALSE) df <- BiocParallel::bplapply(chrs, function(CHR) { mats <- map(hics, ~ .x[CHR] |> interactions() |> gi2cm('count') |> cm2matrix())