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-rw-r--r--.envrc9
-rw-r--r--default.nix17
-rw-r--r--flake.lock42
-rw-r--r--flake.nix19
-rw-r--r--logo-running.pdfbin0 -> 4899 bytes
-rw-r--r--logo.pdfbin0 -> 7899 bytes
-rw-r--r--shell.nix22
-rw-r--r--slides.tex24
-rw-r--r--tex.nix19
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
Binary files differ
diff --git a/logo.pdf b/logo.pdf
new file mode 100644
index 0000000..d5d0526
--- /dev/null
+++ b/logo.pdf
Binary files differ
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
+
+ ;
+}