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{ bionix ? import ./.. {} }:
with bionix;
stage {
name = "tools-docs";
src = ../tools;
xsltFlags = lib.concatStringsSep " " [
#"--param section.autolabel 1"
#"--param section.label.includes.component.label 1"
#"--stringparam html.stylesheet 'style.css overrides.css highlightjs/mono-blue.css'"
#"--stringparam html.script './highlightjs/highlight.pack.js ./highlightjs/loader.js'"
#"--param xref.with.number.and.title 1"
#"--param toc.section.depth 3"
#"--stringparam admon.style ''"
#"--stringparam callout.graphics.extension .svg"
];
buildInputs = with pkgs; [ nixdoc libxslt libxml2 ];
installPhase = ''
function docgen {
nixdoc -c "$1" -d "$2" -f "$1.nix" | sed 's/lib\./bionix./g' |grep -v locations.xml > "$1.xml"
}
docgen ascat 'ascatNGS CNV caller'
docgen bowtie 'Bowtie aligner'
docgen bwa 'BWA aligner'
docgen strelka 'Strelka2 variant caller'
mkdir $out
cp ${./tools.xml} tools.xml
xmllint --nonet --xinclude --noxincludenode tools.xml --output tools-full.xml
cat tools-full.xml
xsltproc $xsltFlags \
--nonet \
--xinclude \
--output $out/index.html \
${pkgs.docbook_xsl_ns}/xml/xsl/docbook/epub/docbook.xsl \
tools-full.xml
'';
}
|
