From d12f635279ec1b43a57293c9c95919a489606d8c Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 11 Jun 2019 16:44:36 +1000
Subject: rewrite README documentation

Significant expansion of README to include installation instructions and
instructions on how to use with HPC.
---
 doc/default.nix   | 47 +++++++++++++++++++++++++++++++++++++++++++++++
 doc/tools-doc.nix | 47 -----------------------------------------------
 2 files changed, 47 insertions(+), 47 deletions(-)
 create mode 100644 doc/default.nix
 delete mode 100644 doc/tools-doc.nix

(limited to 'doc')

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
+  '';
+}
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
-  '';
-}
-- 
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