diff options
| author | Justin Bedo <cu@cua0.org> | 2019-03-06 11:43:19 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-03-06 11:43:19 +1100 |
| commit | a86ef4eda927c47791dc0c25852c13ea622f809b (patch) | |
| tree | e4604cde726ee8d078bb4f62f331ac0f1c256360 /doc | |
| parent | e81641608ffd0b08b8da0d1bf0546bc92d3b4088 (diff) | |
draft API docs for BWA and strelka
Diffstat (limited to 'doc')
| -rw-r--r-- | doc/tools-doc.nix | 41 | ||||
| -rw-r--r-- | doc/tools.xml | 14 |
2 files changed, 55 insertions, 0 deletions
diff --git a/doc/tools-doc.nix b/doc/tools-doc.nix new file mode 100644 index 0000000..b2cd7ba --- /dev/null +++ b/doc/tools-doc.nix @@ -0,0 +1,41 @@ +{ 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 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 + ''; +} diff --git a/doc/tools.xml b/doc/tools.xml new file mode 100644 index 0000000..f23dfeb --- /dev/null +++ b/doc/tools.xml @@ -0,0 +1,14 @@ +<book xmlns="http://docbook.org/ns/docbook" + xmlns:xi="http://www.w3.org/2001/XInclude"> + <info> + <title>Bionix</title> + </info> + <section xmlns="http://docbook.org/ns/docbook" + xmlns:xlink="http://www.w3.org/1999/xlink" + xmlns:xi="http://www.w3.org/2001/XInclude" + xml:id="sec-tools"> + <title>Tools</title> + <xi:include href="bwa.xml" /> + <xi:include href="strelka.xml" /> + </section> +</book> |