Merge pull request #9 from umccr/issues-8/conda

Add bsgenome conda pkgs to sigrap
umccr · Dec 12, 2024 · b65a86e · b65a86e
2 parents fafc9ad + e2ef2db
commit b65a86e
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Showing 7 changed files with 86 additions and 93 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
diff --git a/.bumpversion.toml b/.bumpversion.toml
@@ -0,0 +1,40 @@
+[tool.bumpversion]
+current_version = "0.1.1"
+search = "{current_version}"
+replace = "{new_version}"
+message = "Bump version: {current_version} → {new_version}"
+regex = false
+ignore_missing_version = false
+ignore_missing_files = false
+commit = true
+parse = """(?x)
+    (?P<major>0|[1-9]\\d*)\\.
+    (?P<minor>0|[1-9]\\d*)\\.
+    (?P<patch>0|[1-9]\\d*)
+    (?:\\.(?P<dev>\\d+))?
+"""
+
+serialize = [
+    "{major}.{minor}.{patch}.{dev}",
+    "{major}.{minor}.{patch}",
+]
+
+[[tool.bumpversion.files]]
+filename = "DESCRIPTION"
+search = "Version: {current_version}"
+replace = "Version: {new_version}"
+
+[[tool.bumpversion.files]]
+filename = ".github/workflows/deploy.yaml"
+search = "VERSION: '{current_version}'"
+replace = "VERSION: '{new_version}'"
+
+[[tool.bumpversion.files]]
+filename = "conda/env/yaml/sigrap.yaml"
+search = "r-sigrap =={current_version}"
+replace = "r-sigrap =={new_version}"
+
+[[tool.bumpversion.files]]
+filename = "conda/recipe/meta.yaml"
+search = "version: {current_version}"
+replace = "version: {new_version}"
diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
@@ -24,7 +24,7 @@ jobs:
 
     steps:
       - name: Code checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Miniconda setup
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -91,26 +91,26 @@ jobs:
 
       # work with tag from above
       - name: Code checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: v${{ env.VERSION }}
       - name: 🏰 QEMU setup
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
       - name: 🏯 Buildx setup
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
         with:
           install: true
           config-inline: |
             [worker.oci]
               max-parallelism = 2
       - name: 🐙 GitHub CR login
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
       - name: 🐳 Docker img build and push
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           tags: ghcr.io/${{ github.repository }}:${{ env.VERSION }}
           context: .

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@
 # R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.0
+    rev: v0.4.3
     hooks:
     -   id: style-files
         args: [--style_pkg=styler, --style_fun=tidyverse_style]
@@ -14,7 +14,7 @@ repos:
     -   id: use-tidy-description
     -   id: readme-rmd-rendered
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.2.0
+    rev: v4.6.0
     hooks:
     -   id: check-added-large-files
         args: ['--maxkb=200']

diff --git a/README.Rmd b/README.Rmd
@@ -70,37 +70,22 @@ sigrap_cli=$(Rscript -e 'x = system.file("cli", package = "sigrap"); cat(x, "\n"
 export PATH="${sigrap_cli}:${PATH}"
 ```
 
-```{bash echo=FALSE}
+```{bash prompt=TRUE, echo=FALSE}
 sigrap_cli=$(Rscript -e 'x = system.file("cli", package = "sigrap"); cat(x, "\n")' | xargs)
 export PATH="${sigrap_cli}:${PATH}"
 
-echo "$ sigrap.R --version"
-echo "sigrap.R 0.1.1"
-echo ""
-echo "$ sigrap.R --help"
-sigrap.R --help
-echo ""
+echo "sigrap.R --version" & sigrap.R --version
 echo ""
+echo "#-----------------------------------#"
+echo "sigrap.R --help" & sigrap.R --help
 echo ""
 echo "#------- HRDetect -------#"
-echo ""
-echo ""
-echo "$ sigrap.R hrdetect --help"
-sigrap.R hrdetect --help
-echo ""
-echo ""
+echo "sigrap.R hrdetect --help" & sigrap.R hrdetect --help
 echo ""
 echo "#------- CHORD -------#"
-echo ""
-echo ""
-echo "$ sigrap.R chord --help"
-sigrap.R chord --help
-echo ""
-echo ""
+echo "sigrap.R chord --help" & sigrap.R chord --help
 echo ""
 echo "#------- MutationalPatterns -------#"
 echo ""
-echo ""
-echo "$ sigrap.R mutpat --help"
-sigrap.R mutpat --help
+echo "sigrap.R mutpat --help" & sigrap.R mutpat --help
 ```
diff --git a/README.md b/README.md
@@ -1,12 +1,11 @@
 
--   <a href="#id_-sigrap" id="toc-id_-sigrap">🎶 sigrap</a>
-    -   <a href="#installation" id="toc-installation">Installation</a>
-    -   <a href="#main-modules" id="toc-main-modules">Main Modules</a>
-        -   <a href="#id_-hrdetect" id="toc-id_-hrdetect">🔍 HRDetect</a>
-        -   <a href="#id_-chord" id="toc-id_-chord">🎸 CHORD</a>
-        -   <a href="#id_-mutationalpatterns" id="toc-id_-mutationalpatterns">🐾
-            MutationalPatterns</a>
-    -   <a href="#id_-cli" id="toc-id_-cli">💻 CLI</a>
+- [🎶 sigrap](#id_-sigrap)
+  - [Installation](#installation)
+  - [Main Modules](#main-modules)
+    - [🔍 HRDetect](#id_-hrdetect)
+    - [🎸 CHORD](#id_-chord)
+    - [🐾 MutationalPatterns](#id_-mutationalpatterns)
+  - [💻 CLI](#id_-cli)
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
@@ -15,7 +14,7 @@
 Wrappers for somatic mutation signature analysis tools (HRDetect, CHORD,
 MutationalPatterns).
 
--   Docs: <https://umccr.github.io/sigrap/>
+- Docs: <https://umccr.github.io/sigrap/>
 
 <!-- badges: start -->
 
@@ -29,7 +28,7 @@ install](https://anaconda.org/umccr/r-sigrap/badges/installer/conda.svg)](https:
 remotes::install_github("umccr/sigrap")
 ```
 
--   Or if used inside a conda environment:
+- Or if used inside a conda environment:
 
 ``` bash
 conda install r-sigrap -c umccr -c conda-forge -c bioconda
@@ -61,21 +60,22 @@ see vignette at
 
 A `sigrap` command line interface is available for convenience.
 
--   If you’re using the conda package, the `sigrap.R` command will
-    already be set up inside an activated conda environment.
--   If you’re *not* using the conda package, you need to export the
-    `sigrap/inst/cli/` directory to your `PATH` in order to use
-    `sigrap.R`.
+- If you’re using the conda package, the `sigrap.R` command will already
+  be set up inside an activated conda environment.
+- If you’re *not* using the conda package, you need to export the
+  `sigrap/inst/cli/` directory to your `PATH` in order to use
+  `sigrap.R`.
 
 ``` bash
 sigrap_cli=$(Rscript -e 'x = system.file("cli", package = "sigrap"); cat(x, "\n")' | xargs)
 export PATH="${sigrap_cli}:${PATH}"
 ```
 
-    $ sigrap.R --version
-    sigrap.R 0.1.1
+    sigrap.R --version
+    sigrap 0.1.1
 
-    $ sigrap.R --help
+    #-----------------------------------#
+    sigrap.R --help
     usage: sigrap [-h] [-v] {hrdetect,chord,mutpat} ...
 
     Somatic signature wrappers
@@ -87,51 +87,40 @@ export PATH="${sigrap_cli}:${PATH}"
         chord               CHORD help
         mutpat              MutationalPatterns help
 
-    optional arguments:
+    options:
       -h, --help            show this help message and exit
       -v, --version         show program's version number and exit
 
-
-
     #------- HRDetect -------#
-
-
-    $ sigrap.R hrdetect --help
+    sigrap.R hrdetect --help
     usage: sigrap hrdetect [-h] --sample SAMPLE --snv SNV --sv SV --cnv CNV
                            [--out OUT]
 
-    optional arguments:
+    options:
       -h, --help       show this help message and exit
       --sample SAMPLE  Sample name.
       --snv SNV        Input SNV (VCF format).
       --sv SV          Input SV (VCF format).
       --cnv CNV        Input CNV (TSV format).
       --out OUT        Output file ['hrdetect.json.gz'].
 
-
-
     #------- CHORD -------#
-
-
-    $ sigrap.R chord --help
+    sigrap.R chord --help
     usage: sigrap chord [-h] --sample SAMPLE --snv SNV --sv SV [--out OUT]
 
-    optional arguments:
+    options:
       -h, --help       show this help message and exit
       --sample SAMPLE  Sample name.
       --snv SNV        Input SNV (VCF format).
       --sv SV          Input SV (VCF format).
       --out OUT        Output file ['./chord.json.gz']
 
-
-
     #------- MutationalPatterns -------#
 
-
-    $ sigrap.R mutpat --help
+    sigrap.R mutpat --help
     usage: sigrap mutpat [-h] --sample SAMPLE --snv SNV --outdir OUTDIR
 
-    optional arguments:
+    options:
       -h, --help       show this help message and exit
       --sample SAMPLE  Sample name.
       --snv SNV        Input SNV file (VCF format).

diff --git a/conda/recipe/meta.yaml b/conda/recipe/meta.yaml
@@ -31,6 +31,9 @@ requirements:
     - bioconductor-structuralvariantannotation
     - r-tidyr
     - bioconductor-variantannotation
+    - bioconductor-bsgenome.hsapiens.ucsc.hg38
+    - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene
+    - bioconductor-genomeinfodbdata
   run:
     - r-base
     - r-assertthat
@@ -47,6 +50,9 @@ requirements:
     - bioconductor-structuralvariantannotation
     - r-tidyr
     - bioconductor-variantannotation
+    - bioconductor-bsgenome.hsapiens.ucsc.hg38
+    - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene
+    - bioconductor-genomeinfodbdata
 
 test:
   commands: