rewrite README documentation

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

1 files changed, 0 insertions, 47 deletions

diff --git a/doc/tools-doc.nix b/doc/tools-doc.nix
deleted file mode 100644
index d68a6b1..0000000
--- a/doc/tools-doc.nix
+++ /dev/null
@@ -1,47 +0,0 @@
-{ 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
-  '';
-}