V0.2.0

.Rbuildignore

@@ -1,4 +1,20 @@
-^pipeline_files$
-^tests/testthat/results$
-^tests/testthat/pf_rrbs$
+^renv$
+^renv\.lock$
+^\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$
 ^README\.Rmd$
+^data/.+$
+^docs/.+$
+^fork/.+$
+^tests/.+$
+\.Rprofile
+\.renvignore
+\.here
+\.gitignore
+\.DS_Store
+^_pkgdown\.yml$
+^\.github$
+^test_.*$
+^vignettes/.+$
+^refs/.+$

.gitattributes

@@ -0,0 +1 @@
+docs/** linguist-vendored

.gitignore

@@ -1,9 +1,48 @@
-.lintr
-.vscode
+*.pdf
+*.Rhistory
+.Rhistory
+.RData*
+.Rproj.user
+archive/
+data/
+docs/example_*
+docs/wgbs.nf
+*.tar.gz
 pipeline_files/
-test_result/
-tests/testthat/pf_rrbs
-tests/testthat/results
-tests/testthat/result*
+renv/
+.drake/
+TEST/
+*.RData
+pipeline_files/*
+slurm/
+results/
+transfer.zip
+*./vanloo-main/
+code/**/*.png
+code/**/*.stats
+code/**/*.bigWig
+code/*/*
+camdac_paper/
+*.drawio
+*.docx
+.DS_Store
+.here
+.Rprofile
 man/
-CAMDAC_manual/manual_figures/*.svg
+inst/doc
+*.json
+temp/
+wgbs_test/
+test_*.R
+.lintr
+*.code-workspace
+*dev.md
+tests/testthat/result*
+local/
+wgbs_asm/
+test_wgbs_asm/
+result*
+CAMDAC_manual/
+*.log.lintr
+data/
+bin/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: CAMDAC
 Title: Copy-number Aware Methylation Deconvolution and Analysis of Cancers
-Version: 0.1.0
+Version: 0.2.0
 Authors@R: 
     c(
     person(given = "Elizabeth",
@@ -10,6 +10,9 @@ Authors@R:
            family = "Mensah",
            role = c("aut", "cre"),
            email="nana.mensah@crick.ac.uk"),
+    person(given = "Siqi",
+           family = "Lai",
+           role = c("aut")),
     person(given = "Carla",
            family = "Castignani",
            role = c("aut")),
@@ -25,44 +28,52 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.2
+RoxygenNote: 7.3.1
 Suggests: 
-    testthat (>= 3.0.0),
-    devtools,
+    testthat,
     pryr,
+    devtools,
     tictoc,
     mockr,
     tidyr,
     knitr,
     rmarkdown,
-    pkgdown,
-    usethis
+    rcmdcheck
 biocViews:
 Imports: 
+    Rsamtools,
+    fs,
+    qs,
+    fst,
+    parallel,
+    doParallel,
+    gtable,
+    stats,
     optparse,
-    logger
-Depends: 
-    R (>= 3.6.2),
-    ASCAT,
-    stringr,
+    readr,
+    scales,
+    rtracklayer,
+    R.utils,
+    Battenberg,
+    data.table (>= 1.14.6),
+    foreach,
     GenomicRanges,
     GenomicAlignments,
-    Rsamtools,
-    scales,
+    GenomeInfoDb,
+    IRanges,
+    S4Vectors,
+    logging,
     ggplot2,
-    gridExtra,
-    gtable,
-    data.table,
-    readr,
     dplyr,
-    parallel,
-    doParallel,
-    devtools,
-    fst,
-    fs,
+    gridExtra,
+    grid,
+    stringr,
     png,
-    grid
-Remotes: VanLoo-Lab/ascat/ASCAT@v3.2.0,
-VignetteBuilder: knitr
-Config/testthat/edition: 3
-Config/testthat/start-first: test_download*
+    MASS,
+    ASCAT (>= 3.0.0)
+Depends:
+    R (>= 3.6.2)
+Remotes: 
+    Battenberg=NMNS93/battenberg@dev-ascat3,
+    ASCAT=Vanloo-Lab/ascat/ASCAT/@44ddd3080723a2c3640d1cfead13437a093c21d1
+VignetteBuilder: rmarkdown

Dockerfile

@@ -0,0 +1,49 @@
+# Use a lightweight R base image
+FROM rocker/r-ver:4.4.0
+# Set the working directory
+WORKDIR /app
+
+# Install system dependencies (if needed)
+# For example, if your package needs external libraries, install them here
+RUN chmod 1777 /tmp
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+    && apt-get install -y libxml2 libodbc1 \
+    && apt-get install -y libz-dev libbz2-dev bzip2-doc zlib1g-dev \
+    && apt-get install -y liblzma-dev libcurl4-openssl-dev wget \
+    && apt-get install -y default-jre git curl bzip2 pandoc
+
+# Install alleleCounter
+RUN git clone https://github.com/cancerit/alleleCount.git \
+    && cd alleleCount && bash ./setup.sh /usr/local
+RUN echo 'export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH' >> ~/.bashrc
+RUN echo 'export PATH=/usr/local/bin:$PATH' >> ~/.bashrc
+
+# Set WORKDIR
+WORKDIR /app
+
+# Install CAMDAC
+RUN R -q -e 'install.packages("remotes")'
+RUN R -q -e 'install.packages("devtools")'
+
+# Create ~/.R directory and configure Makevars file for R-specific flags.
+#   Required for bioconductor packages used in Battenberg install.
+RUN mkdir -p /root/.R && \
+    echo 'CXXFLAGS=-Wall -Wno-format-security' >> /root/.R/Makevars && \
+    echo 'CFLAGS=-Wall -Wno-format-security' >> /root/.R/Makevars
+
+# Copy only DESCRIPTION and (optionally) NAMESPACE to install deps first
+COPY DESCRIPTION NAMESPACE* ./
+RUN R -q -e 'remotes::install_deps(".", dependencies = TRUE, upgrade = "never", lib = "/usr/local/lib/R/site-library")'
+
+# Generate docs
+RUN R -q -e 'devtools::document()'
+
+# Install CAMDAC from local directories
+COPY R ./R/
+COPY vignettes ./vignettes/
+COPY man ./man/
+RUN Rscript -e 'remotes::install_local(".",  dependencies = TRUE, upgrade = "never", lib = "/usr/local/lib/R/site-library")'
+
+# Set command to be use
+CMD ["/usr/local/bin/Rscript"]