rewrite README documentation

Significant expansion of README to include installation instructions and
instructions on how to use with HPC.

1 files changed, 47 insertions, 0 deletions

diff --git a/doc/default.nix b/doc/default.nix
new file mode 100644
index 0000000..d68a6b1
--- /dev/null
+++ b/doc/default.nix
@@ -0,0 +1,47 @@
+{ 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 cnvkit 'CNVkit CNV caller'
+    docgen facets 'Facets CNV caller'
+    docgen fastqc 'FastQC quality control'
+    docgen gridss 'GRIDSS SV caller'
+    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
+  '';
+}