Automatically download a statically-linked copy of Pandoc during `mak…

…e deps`

This removes a big (optional) dep and makes it easier to generate
documentation on a variety of machines.  It also guarantees us a
specific version.

.gitignore

@@ -3,4 +3,5 @@
 /bin/liftOver.Linux
 /config_local.*
 /bin/cpanm
+/bin/pandoc
 /local

Makefile

@@ -5,19 +5,25 @@ export SHELLOPTS:=errexit:pipefail
 SYS  := $(shell uname -s)
 ARCH := $(shell uname -m)
 
+PANDOC_VERSION ?= 2.1.1
+
 ifeq ($(SYS), Darwin)
-OS := macOSX
+LIFTOVER_SYS   := macOSX
+PANDOC_PKG     := pandoc-$(PANDOC_VERSION)-macOS.zip
+PANDOC_EXTRACT := unzip -DD -o
 else ifeq ($(SYS), Linux)
-OS := linux
+LIFTOVER_SYS   := linux
+PANDOC_PKG     := pandoc-$(PANDOC_VERSION)-linux.tar.gz
+PANDOC_EXTRACT := tar xzvmf
 else
-OS := $(SYS)
+LIFTOVER_SYS := $(SYS)
 endif
 
 cpanm := bin/cpanm
 
 curl := curl -fsSL
 
-deps: $(cpanm) liftover perl-deps hg-data
+deps: $(cpanm) pandoc liftover perl-deps hg-data
 
 perl-deps: cpanfile
 	mkdir -p local
@@ -27,6 +33,19 @@ $(cpanm):
 	$(curl) https://raw.githubusercontent.com/miyagawa/cpanminus/master/cpanm > $@
 	chmod +x $@
 
+pandoc: bin/pandoc
+
+bin/pandoc: cache/pandoc-$(PANDOC_VERSION)/bin/pandoc
+	ln -snvf ../$< $@
+
+cache/pandoc-$(PANDOC_VERSION)/bin/pandoc: cache/$(PANDOC_PKG)
+	cd cache && $(PANDOC_EXTRACT) $(<:cache/%=%) $(@:cache/%=%)
+	chmod +x $@
+
+cache/$(PANDOC_PKG):
+	mkdir -p cache
+	$(curl) https://github.com/jgm/pandoc/releases/download/$(PANDOC_VERSION)/$(PANDOC_PKG) > $@
+
 liftover: bin/liftOver.$(SYS) cache/hg19ToHg38.over.chain.gz
 
 bin/liftOver.$(SYS):
@@ -35,7 +54,7 @@ bin/liftOver.$(SYS):
 	@echo
 	@echo "Type Ctrl-C (^C) to abort or enter to proceed."
 	@read
-	$(curl) http://hgdownload.soe.ucsc.edu/admin/exe/$(OS).$(ARCH)/liftOver > $@
+	$(curl) http://hgdownload.soe.ucsc.edu/admin/exe/$(LIFTOVER_SYS).$(ARCH)/liftOver > $@
 	chmod +x $@
 
 cache/hg19ToHg38.over.chain.gz:

bin/generate-website

@@ -226,7 +226,7 @@ if [[ $refresh_docs == yes ]]; then
     done
 
     if [[ $doc_failed -eq 1 ]]; then
-        echo "Warning: Couldn't generate documentation, but succeeding anyway. Is pandoc installed?"
+        echo "Warning: Couldn't generate documentation but continuing on…"
     fi
 
     echo "Indexing documentation"

doc/Install.md

@@ -20,8 +20,7 @@ contacting a local expert familiar with your computing systems.
 
 [Perl](https://www.perl.org) 5.14 or later, standard Unix tools including
 `make`, and [libcurl](https://curl.haxx.se) are all required to run the ISDB
-tools. [Pandoc](http://pandoc.org) 2.0 or later is used for generating
-documentation web pages. It is optional but recommended.
+tools.
 
 ISDB is designed to use [PostgreSQL](https://www.postgresql.org) as the
 database server. You must either have "superuser" access to a PostgreSQL
@@ -33,17 +32,14 @@ server, or access to the owner role of a database set up for your use.
 
 2. Download and install [Postgres.app](http://postgresapp.com)
 
-3. Install [pandoc](http://pandoc.org/installing.html) with its installer
-   package
-
 MacOS versions starting with 10.9 (Mavericks), released in 2013, include a
 sufficiently new version of Perl to run all the ISDB tools. libcurl is included
 with macOS as well.
 
 ## Installing prerequisites on Debian or Ubuntu
 
 1. Install packaged dependencies:
-   `apt-get install build-essential pkg-config libcurl4-gnutls-dev pandoc`
+   `apt-get install build-essential pkg-config libcurl4-gnutls-dev`
 
 2. Set up the PostgreSQL APT repository appropriate for your system
    [Debian](https://www.postgresql.org/download/linux/debian/),
@@ -62,7 +58,7 @@ These instructions should also work on Fedora and other RHEL variants, although
 they've only been tested on CentOS 7.
 
 1. Install packaged dependencies:
-   `yum install @development libcurl-devel pandoc perl-core`
+   `yum install @development libcurl-devel perl-core`
 
 2. Set up the [PostgreSQL yum repository](https://www.postgresql.org/download/linux/redhat/)
    for at least Pg 9.4 or newer following their instructions
@@ -83,6 +79,7 @@ directory:
 * The UCSC Genome Browser's `liftOver` tool
 * The `liftOver` chain file for mapping hg19 to hg38 coordinates
 * Gene annotation and chromosome metadata from the [NCBI](https://www.ncbi.nlm.nih.gov)
+* [Pandoc](http://pandoc.org) for generating documentation web pages
 
 # Create the database