Merge pull request #125 from umccr/deploy_0.5.0

Deploy conda pkg and Docker image

.bumpversion.cfg

@@ -1,6 +1,10 @@
 [bumpversion]
-current_version = 0.4.9
+current_version = 0.5.0
 commit = True
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<dev>\d+))?
+serialize = 
+	{major}.{minor}.{patch}.{dev}
+	{major}.{minor}.{patch}
 
 [bumpversion:file:DESCRIPTION]
 search = Version: {current_version}

.github/workflows/conda_docker_pkgdown.yml

@@ -3,13 +3,14 @@ name: conda-docker-docs
 on:
   push:
     branches:
-      - conda
+      - deploy_0.5.0
+      - rnasum-rpackage
 env:
   atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }}
   recipe_path: deploy/conda/recipe
   env_yaml_path: deploy/conda/env/yaml
   env_lock_path: deploy/conda/env/lock
-  VERSION: '0.4.9' # versioned by bump2version
+  VERSION: '0.5.0' # versioned by bump2version
 
 jobs:
   condarise-dockerise-document:
@@ -27,21 +28,23 @@ jobs:
       - name: Micromamba setup
         uses: mamba-org/setup-micromamba@v1
         with:
-          micromamba-version: '1.4.9-0'
           environment-file: ${{ env.env_yaml_path }}/condabuild.yaml
       - name: 🐍 Conda pkg build and upload
         run: |
-          conda mambabuild --R 4.2 ${recipe_path} --token ${atoken}
+          conda mambabuild ${recipe_path} -c umccr -c conda-forge -c bioconda --token ${atoken}
       - name: 🔒 Conda lock
         run: |
-          conda-lock --file ${env_yaml_path}/rnasum.yaml --platform linux-64
-          mv conda-lock.yml ${env_lock_path}/conda-lock.yml
+          # 1. generate a combined lock file
+          # 2. render platform-specific locks
+          conda-lock lock --file ${env_yaml_path}/rnasum.yaml -p osx-64 -p linux-64
+          conda-lock render --kind explicit -p osx-64 -p linux-64 conda-lock.yml --filename-template 'rnasum-{platform}.lock' && rm conda-lock.yml
+          mv rnasum-*.lock ${env_lock_path}/
       - name: 💾 Commit lockfile
         run: |
           git status
           git config --local user.email "[email protected]"
           git config --local user.name "GitHub Actions"
-          MSG="[bot] Updating conda-lock file (v${VERSION})"
+          MSG="[bot] Updating conda-lock files (v${VERSION})"
           git add .
           git commit -m "${MSG}"
           git push

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RNAsum
 Title: A Robust Tool for Performing Transcriptome Profiling on Cancer Data
-Version: 0.4.9
+Version: 0.5.0
 Authors@R: 
     c(person(given = "Sehrish",
              family = "Kanwal",

Dockerfile

@@ -12,10 +12,10 @@ RUN mamba config \
     mamba clean --all --force-pkgs-dirs
 
 ARG ENV_NAME="rnasum_env"
-COPY ./deploy/conda/env/lock/conda-lock.yml .
-RUN conda-lock install --name ${ENV_NAME} conda-lock.yml && \
-    mamba clean --all --force-pkgs-dirs && \
-    rm conda-lock.yml
+ARG LOCK_FILE="rnasum-linux-64.lock"
+COPY ./deploy/conda/env/lock/${LOCK_FILE} .
+RUN conda-lock install --name ${ENV_NAME} ${LOCK_FILE} && \
+    mamba clean --all --force-pkgs-dirs
 
 ARG MAMBA_PREFIX="/opt/conda"
 ENV PATH="${MAMBA_PREFIX}/envs/${ENV_NAME}/bin:${PATH}"

deploy/conda/env/yaml/rnasum.yaml

@@ -6,4 +6,4 @@ channels:
   - bioconda
 
 dependencies:
-  - r-rnasum ==0.4.9 # versioned by bump2version
+  - r-rnasum ==0.5.0 # versioned by bump2version

deploy/conda/recipe/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: r-rnasum
-  version: 0.4.9 # bump2version
+  version: 0.5.0 # bump2version
 
 source:
   path: ../../../
@@ -31,12 +31,12 @@ requirements:
     - r-ggforce
     - r-ggplot2
     - r-glue
-    - r-gpgr
+    - umccr::r-gpgr
     - r-htmltools
     - r-htmlwidgets
     - r-knitr
     - bioconductor-limma ==3.50.1
-    - r-manhattanly # grab for R v4.1 from umccr
+    - umccr::r-manhattanly # grab for R v4.1 from umccr
     - r-matrixstats ==0.61.0
     - r-optparse
     - r-pdftools
@@ -48,7 +48,7 @@ requirements:
     - r-readr
     - r-rlang
     - r-rmarkdown
-    - r-rnasum.data
+    - umccr::r-rnasum.data
     - r-scales
     - r-sessioninfo
     - r-stringr
@@ -71,12 +71,12 @@ requirements:
     - r-ggforce
     - r-ggplot2
     - r-glue
-    - r-gpgr
+    - umccr::r-gpgr
     - r-htmltools
     - r-htmlwidgets
     - r-knitr
     - bioconductor-limma ==3.50.1
-    - r-manhattanly # grab for R v4.1 from umccr
+    - umccr::r-manhattanly # grab for R v4.1 from umccr
     - r-matrixstats ==0.61.0
     - r-optparse
     - r-pdftools
@@ -88,7 +88,7 @@ requirements:
     - r-readr
     - r-rlang
     - r-rmarkdown
-    - r-rnasum.data
+    - umccr::r-rnasum.data
     - r-scales
     - r-sessioninfo
     - r-stringr

inst/cli/rnasum.R

@@ -27,7 +27,7 @@ option_list <- list(
   make_option("--drugs", action = "store_true", help = "Include drug matching section in report."),
   make_option("--filter", action = "store_true", help = "Filter out low expressed genes."),
   make_option("--immunogram", action = "store_true", help = "Include immunogram in report."),
-  make_option("--log", action = "store_true", default = TRUE, help = "Log2 transform data before normalisation."),
+  make_option("--log", action = "store_true", help = "Log2 transform data before normalisation."),
   make_option("--manta_tsv", type = "character", help = "File path to umccrise 'manta.tsv' output."),
   make_option("--norm", type = "character", help = "Normalisation method."),
   make_option("--pcgr_splice_vars", action = "store_true", help = "Include non-coding splice region variants reported in PCGR."),
@@ -45,8 +45,7 @@ option_list <- list(
   make_option("--top_genes", default = 5, type = "integer", help = "Number of top ranked genes to be presented in report."),
   make_option("--transform", default = "CPM", type = "character", help = "Transformation method to be used when converting read counts. [def: %default]"),
   make_option("--umccrise", type = "character", help = "Directory path of the corresponding WGS-related umccrise data."),
-  make_option(c("--version", "-v"), action = "store_true", help = "Print RNAsum version and exit."),
-  make_option("--html_dir", type = "character", default = getwd(), help = "Directory path to output final HTML report. [def: current directory (%default)]")
+  make_option(c("--version", "-v"), action = "store_true", help = "Print RNAsum version and exit.")
 )
 
 parser <- optparse::OptionParser(option_list = option_list, formatter = optparse::TitledHelpFormatter)
@@ -59,8 +58,6 @@ if (!is.null(opt$version)) {
 # don't need these any more so NULLify to remove from params
 opt$version <- NULL
 opt$help <- NULL
-html_dir <- opt$html_dir
-opt$html_dir <- NULL
 
 ##### Convert missing flags to FALSE
 flags <- c("batch_rm", "dataset_name_incl", "drugs", "filter", "immunogram", "log", "pcgr_splice_vars", "save_tables")
@@ -114,7 +111,7 @@ if (opt$transform == "TPM" && !(opt$norm %in% c("quantile", "none"))) {
 dataset_name_incl <- ifelse(opt$dataset_name_incl, glue::glue("_{opt$dataset}"), "")
 out_file_base <- glue::glue("{opt$sample_name}{toupper(dataset_name_incl)}.RNAseq_report")
 out_html <- RNAsum::rnasum_rmd(
-  out_file = file.path(html_dir, glue::glue("{out_file_base}.html")),
+  out_file = file.path(opt$report_dir, glue::glue("{out_file_base}.html")),
   pars = opt
 )
 message(glue::glue("RNAsum HTML output at: {out_html}"))