init

9 files changed, 152 insertions, 0 deletions

diff --git a/.envrc b/.envrc
new file mode 100644
index 0000000..dc4ab2a
--- /dev/null
+++ b/.envrc
@@ -0,0 +1,9 @@
+use_flake() {
+  watch_file flake.nix
+  watch_file flake.lock
+  watch_file shell.nix
+  watch_file default.nix
+  watch_file tex.nix
+  eval "$(nix print-dev-env)"
+}
+use flake
diff --git a/default.nix b/default.nix
new file mode 100644
index 0000000..5ba0079
--- /dev/null
+++ b/default.nix
@@ -0,0 +1,17 @@
+{ pkgs ? import <nixpkgs> {}, rev ? null }:
+
+with pkgs;
+
+stdenv.mkDerivation {
+  name = "bionix-slides";
+  src = ./.;
+  buildInputs = with pkgs; [ exiftool (callPackage ./tex.nix {}) ];
+  buildPhase = ''
+    latexmk -xelatex slides
+    ${lib.optionalString (rev != null) "exiftool -Producer='${rev}' slides.pdf"}
+  '';
+  installPhase = ''
+    mkdir -p $out
+    cp slides.pdf $out
+  '';
+}
diff --git a/flake.lock b/flake.lock
new file mode 100644
index 0000000..792dc2c
--- /dev/null
+++ b/flake.lock
@@ -0,0 +1,42 @@
+{
+  "nodes": {
+    "flake-utils": {
+      "locked": {
+        "lastModified": 1601282935,
+        "narHash": "sha256-WQAFV6sGGQxrRs3a+/Yj9xUYvhTpukQJIcMbIi7LCJ4=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "588973065fce51f4763287f0fda87a174d78bf48",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1604275927,
+        "narHash": "sha256-Hzd/L9+NuDjSjkqa70vUFZYE7+DFrpO9mghJd3/l1pw=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "6a563e121f5b740308714c9d14c3527b8ba1816b",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "flake-utils": "flake-utils",
+        "nixpkgs": "nixpkgs"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}
diff --git a/flake.nix b/flake.nix
new file mode 100644
index 0000000..f019bad
--- /dev/null
+++ b/flake.nix
@@ -0,0 +1,19 @@
+{
+  description = "BioNix paper";
+  inputs.nixpkgs.url = "github:NixOS/nixpkgs";
+  inputs.flake-utils.url = "github:numtide/flake-utils";
+
+  outputs = { self, nixpkgs, flake-utils, ... }:
+    flake-utils.lib.eachDefaultSystem (system:
+      let pkgs = nixpkgs.legacyPackages.${system};
+      in {
+        devShell = import ./shell.nix { inherit pkgs; };
+        defaultPackage = if self ? rev then
+          import ./default.nix {
+            inherit (self) rev;
+            inherit pkgs;
+          }
+        else
+          throw "Refusing to build in dirty tree";
+      });
+}
diff --git a/logo-running.pdf b/logo-running.pdf
new file mode 100644
index 0000000..600c616
--- /dev/null
+++ b/logo-running.pdf
diff --git a/logo.pdf b/logo.pdf
new file mode 100644
index 0000000..d5d0526
--- /dev/null
+++ b/logo.pdf
diff --git a/shell.nix b/shell.nix
new file mode 100644
index 0000000..75e06bd
--- /dev/null
+++ b/shell.nix
@@ -0,0 +1,22 @@
+{ pkgs ? import <nixpkgs> {} }:
+
+with pkgs;
+
+let
+  style-check =
+    stdenv.mkDerivation rec {
+      name = "style-check";
+      src = fetchurl {
+        url = "http://www.cs.umd.edu/~nspring/software/style-check-current.tar.gz";
+        sha256 = "06g1ni28fdbrg2yaa6x8z3kg1mrjvhi48qv45hb80fwyrvy0ds1a";
+      };
+      installPhase = ''
+        make PREFIX=$out SYSCONFDIR=$out/etc/style-check.d/ install
+        sed -ie "s|/etc/style-check.d|$out/etc/style-check.d|g" $out/bin/style-check.rb
+      '';
+      buildInputs = [ ruby ];
+    };
+
+in mkShell {
+  buildInputs = with pkgs; [ (callPackage ./tex.nix {}) style-check proselint pandoc ];
+}
diff --git a/slides.tex b/slides.tex
new file mode 100644
index 0000000..3cee3a1
--- /dev/null
+++ b/slides.tex
@@ -0,0 +1,24 @@
+\documentclass[aspectratio=169]{beamer}
+
+\usepackage{microtype}
+
+\definecolor{bngreen}{HTML}{3c8e64}
+%\setbeamercolor*{structure}{bg=white,fg=bngreen}
+\usecolortheme[named=bngreen]{structure}
+\setbeamertemplate{navigation symbols}{}
+\setbeamertemplate{headline}{\hfill\includegraphics[width=.7cm]{logo-running}\hspace{0.1cm}\vspace{-.7cm}}
+
+\author{Justin Bed\H{o}\\WEHI}
+\title{\includegraphics[width=.7\linewidth]{logo}\\functional, reproducible bioinformatics workflows}
+\date{November 10, 2020}
+
+\begin{document}
+
+{
+  \setbeamertemplate{headline}{}
+  \begin{frame}
+    \maketitle
+  \end{frame}
+}
+
+\end{document}
diff --git a/tex.nix b/tex.nix
new file mode 100644
index 0000000..3206be2
--- /dev/null
+++ b/tex.nix
@@ -0,0 +1,19 @@
+{ texlive }:
+
+texlive.combine {
+  inherit (texlive)
+    scheme-minimal latexmk tools collection-xetex collection-fontsrecommended
+    biber latexdiff
+
+    abstract acronym alphalph atbegshi atveryend auxhook biblatex bigfoot
+    booktabs caption cleveref colortbl doi enumitem environ etexcmds etoolbox
+    eulervm fancyhdr fontspec footmisc geometry gettitlestring graphics hycolor
+    hyperref hyphenat infwarerr koma-script kvdefinekeys kvoptions kvsetkeys
+    lastpage logreq ltxcmds mathastext mdframed merriweather microtype nag
+    needspace newfloat newunicodechar pdftexcmds pgf preprint quoting ragged2e
+    relsize rerunfilecheck scalerel stringenc sttools textpos titlesec
+    trimspaces url xcolor xkeyval xpatch xstring zref listings oberdiek
+    beamer
+
+  ;
+}