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install chrome, and modify quarto report generation #19

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23 changes: 3 additions & 20 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -7,26 +7,9 @@ RUN conda config --set channel_priority strict
## install snakemake
RUN mamba install -y -c conda-forge -c bioconda snakemake graphviz

# install chrome dependencies (for kaleido/plotly to export plot .png/.svg)
RUN apt update && apt-get install -y \
libnss3 \
libatk-bridge2.0-0 \
libcups2 \
libxcomposite1 \
libxdamage1 \
libxfixes3 \
libxrandr2 \
libgbm1 \
libxkbcommon0 \
libpango-1.0-0 \
libcairo2

# install python packages
RUN pip install --upgrade pip
RUN pip install kaleido

# install chrome for kaleido
RUN kaleido_get_chrome
# download + install Google Chrome (for kaleido/plotly to export plot .png/.svg)
RUN wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb
RUN apt-get update && apt install -y ./google-chrome-stable_current_amd64.deb

## copy the pipeline code into the container
WORKDIR /app
Expand Down
11 changes: 6 additions & 5 deletions app/workflow/Snakefile
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Expand Up @@ -103,7 +103,7 @@ VERSION_ENVS = [

# ********** Quarto reports **********
QMD_FILES = glob(os.path.join(REPORTS_DIR, "**", "*.qmd"), recursive=True) if REPORTS_DIR else []
QUARTO_HTML_FILES = [STEP_QUARTO_DIR + os.path.basename(os.path.dirname(f)) + "/" + os.path.splitext(os.path.basename(f))[0] + ".html" for f in QMD_FILES]
QUARTO_HTML_FILES = [STEP_QUARTO_DIR + os.path.splitext(os.path.basename(qmd))[0] + ".html" for qmd in QMD_FILES]

# ********** helper functions to get R1/R2 FASTQ files **********
def get_r1(wildcards):
Expand Down Expand Up @@ -990,21 +990,22 @@ rule prose:
############# Last step: Re-generate user-defined Quarto reports #############
rule render_quarto:
input:
qmd_path=REPORTS_DIR + "{dir_name}/{qmd_name}.qmd",
qmd_path=REPORTS_DIR + "{qmd_name}.qmd",
methods=STEP_PROSE_DIR + "methods.md", # not used; runs Quarto as the last step
output:
STEP_QUARTO_DIR + "{dir_name}/{qmd_name}.html",
STEP_QUARTO_DIR + "{qmd_name}.html",
threads:
CORES
conda:
"envs/quarto.yml"
log:
LOGS + Path(STEP_QUARTO_DIR).name + "/{dir_name}/{qmd_name}.log",
LOGS + Path(STEP_QUARTO_DIR).name + "/{qmd_name}.log",
shell:
# Quarto writes the rendered HTML next to the source .qmd; move it into
# the results reports dir so it matches the declared output. (Quarto's
# --output-dir is resolved relative to the input file, so it can't be
# pointed straight at an arbitrary results path.)
"""
quarto render {input.qmd_path} -M embed-resources:true &> {log}
mkdir -p "$(dirname {output})"
mv "$(dirname {input.qmd_path})/{wildcards.qmd_name}.html" "{output}"
"""