diff --git a/.gitignore b/.gitignore
index 938d2aee..100ca39e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,3 +4,9 @@ syntax: glob
 *.*.swp
 *.tar.gz
 image/Dockerfile
+
+*/*/Dockerfile
+*/*/build.sh
+
+*/build.log
+*.gz
diff --git a/README.md b/README.md
index 1193c47f..75978e3a 100644
--- a/README.md
+++ b/README.md
@@ -5,36 +5,57 @@ Things you can do with docker-build:
 - Build [Galaxy Tool Shed](https://toolshed.g2.bx.psu.edu) dependencies
 - Rebuild Debian or Ubuntu source packages (for modifications)
 
+To use, install Docker. Then for building packages there are two scripts that
+can be used, depending on the package recipes available:
+
+```console
+$ ./build.sh <package>
+$ python build.py <package> --version 1.0
+```
+
+The `build.sh` is the older format, and simply uses a single
+`<package>build.sh` file, like [Atlas](Atlas/). The `build.py` is the newer
+format, and uses yaml metadata in `<package>/<version>/build.yml`.
+
 The base image for Galaxy packages is Debian Squeeze. This will hopefully
 produce binaries usable on Galaxy's targeted platforms (at time of writing:
 CentOS 6+, Debian 6.0+, Ubuntu 12.04+).
 
-To use, install Docker. Then, for Tool Shed dependencies:
+To use, install Docker. Then, for Tool Shed dependencies, e.g.
 
 ```console
 $ ./build galaxy <package>
-```
-e.g.
-
-```console
-$ ./build galaxy samtools
+$ python build.py <package>
 ```
 
-For building dpkgs, use:
+To build packages against a different OS, you can use the `--image` flag, e.g.:
 
 ```console
 $ ./build <dist>[:tag] <package>
+$ python build.py <package> --image <dist>[:tag]
 ```
 
-e.g.:
+e.g.
 
 ```console
 $ ./build ubuntu:trusty nginx
+$ python build.py nginx --image debian:squeeze
 ```
 
+# Building all the things
+
+There's a separate `build-all.sh` which allows you to build all of the packages using their preferred build mechanism
+
+# Notes on the two build scripts
+
+## `build.py`
+
+The `<version>` option is optional, and defaults to the string 'default', which
+is useful for recipes that don't have version specific changes (E.g. bcftools 1.0 builds
+identically to 1.2)
+
+
 ## TODO
 
 - The build scripts themselves are targeted at whatever specific dist/release I
   am building them for at the moment and are not generalized to work on others.
-- Some things in the build scripts probably belong in some sort of build script
-  library.
diff --git a/atlas/default/build.yml b/atlas/default/build.yml
new file mode 100644
index 00000000..d6f87519
--- /dev/null
+++ b/atlas/default/build.yml
@@ -0,0 +1,40 @@
+meta:
+    image: 'debian:squeeze'
+    version: 3.10.2
+prebuild:
+    packages: |
+        libgfortran3
+build:
+    urls:
+        - http://downloads.sourceforge.net/project/math-atlas/Stable/${version}/atlas${version}.tar.bz2
+        - http://www.netlib.org/lapack/lapack-3.5.0.tgz
+    commands:
+        - tar jxf atlas${version}.tar.bz2
+        - cd ATLAS
+        - patch -p1 </host/static_full_blas_lapack.diff
+        - patch -p1 </host/shared_libraries.diff
+        - patch -p1 </host/cpu-throttling-check.diff
+        - cd /build/
+        - |
+            ATLAS/configure \
+                --prefix="/build/dest" \
+                -D c -DWALL \
+                -b 64 \
+                -Fa alg '-fPIC' \
+                -Ss f77lib "-L$(gcc -print-search-dirs|grep ^install:|awk '{print $2}') -lgfortran -lgcc_s -lpthread"  \
+                --with-netlib-lapack-tarfile=/build/lapack-3.5.0.tgz \
+                -A 14 \
+                -V 384 \
+                -v 2 \
+                -t 0 \
+                -Ss ADdir ../../archdefs/amd64 \
+                -Si cputhrchk 0
+        - make
+        - make install
+        - libgfortran=$(readlink -f $(gcc -print-search-dirs|grep ^install:|awk '{print $2}')/libgfortran.so)
+        - basename_libgfortran=$(basename $libgfortran)
+        - libgfortran_version=${basename_libgfortran#"libgfortran.so."}
+        - cp $libgfortran /build/dest/lib
+        - ln -s $(basename $libgfortran) /build/dest/lib/libgfortran.so.${libgfortran_version:0:1}
+        - ln -s libgfortran.so.${libgfortran_version:0:1} /build/dest/lib/libgfortran.so
+        - tar zcf /host/atlas-${version}-Linux-x86_64.tar.gz -C /build/dest .
diff --git a/atlas/default/cpu-throttling-check.diff b/atlas/default/cpu-throttling-check.diff
new file mode 100644
index 00000000..20b9df21
--- /dev/null
+++ b/atlas/default/cpu-throttling-check.diff
@@ -0,0 +1,30 @@
+Description: Reenable the configuration flag for disable CPU throttling check
+ For the generic package, we need the ability to compile on machines with CPU
+ throttling enabled (since some buildds have that feature).
+Author: Sébastien Villemot <sebastien@debian.org>
+Forwarded: not-needed
+Last-Update: 2013-06-11
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- a/CONFIG/src/config.c
++++ b/CONFIG/src/config.c
+@@ -928,10 +928,8 @@
+         "      -Si nocygwin <0/1> : Do/don't depend on GPL cygwin library\n");
+       fprintf(stderr,
+         "                           (Windows compiler/cygwin install only)\n");
+-/* Disabled due to abuse
+       fprintf(stderr,
+         "      -Si cputhrchk <0/1> : Ignore/heed CPU throttle probe\n");
+- */
+       fprintf(stderr,
+            "   -tl <#> <list> : set # of threads, use list of affinity IDs\n");
+       fprintf(stderr,
+@@ -1129,6 +1127,8 @@
+             *NoF77 = k;
+          else if (!strcmp(sp0, "nocygwin"))
+             *NoCygwin = k;
++         else if (!strcmp(sp0, "cputhrchk"))
++            *ThrChk = k;
+          else if (!strcmp(sp0, "kern"))
+             gcc3 = sp;
+          else if (!strcmp(sp0, "ADdir") || !strcmp(sp0, "addir"))
diff --git a/atlas/default/shared_libraries.diff b/atlas/default/shared_libraries.diff
new file mode 100644
index 00000000..f4b6e1c3
--- /dev/null
+++ b/atlas/default/shared_libraries.diff
@@ -0,0 +1,130 @@
+Description: Create shared versions of the libraries
+Author: David Evans
+        Sébastien Villemot <sebastien@debian.org>
+Last-Update: 2014-07-16
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- a/makes/Make.lib
++++ b/makes/Make.lib
+@@ -33,6 +33,79 @@ $(tarnam).tar.bz2 :
+ 	rm -rf $(ARCH)
+ 	$(BZIP) --best $(tarnam).tar
+ 
++fullshared: libatlas.so libcblas.so libf77blas.so liblapack.so atlas/libblas.so atlas/liblapack.so
++
++libatlas.so: libatlas.so.3
++	ln -sf $< $@ 
++
++libatlas.so.3: libatlas.so.3.0
++	ln -sf $< $@ 
++
++libatlas.so.3.0 : libatlas.a
++	ld $(LDFLAGS) -shared -soname libatlas.so.3 -o $@ \
++        --whole-archive libatlas.a --no-whole-archive -lc $(LIBS) $(F77SYSLIB)
++
++libcblas.so: libcblas.so.3
++	ln -sf $< $@ 
++
++libcblas.so.3: libcblas.so.3.0
++	ln -sf $< $@ 
++
++libcblas.so.3.0 : libcblas.a libatlas.so
++	ld $(LDFLAGS) -shared -soname libcblas.so.3 -o $@ \
++	  --whole-archive libcblas.a \
++          --no-whole-archive -L. -latlas $(F77SYSLIB) -lm -lc
++
++libf77blas.so: libf77blas.so.3
++	ln -sf $< $@ 
++
++libf77blas.so.3: libf77blas.so.3.0
++	ln -sf $< $@ 
++
++libf77blas.so.3.0 : libf77blas.a libcblas.so libatlas.so
++	ld $(LDFLAGS) -shared -soname libf77blas.so.3 -o $@ \
++	  --whole-archive libf77blas.a \
++          --no-whole-archive -L. -lcblas -latlas $(F77SYSLIB) -lm -lc
++
++liblapack.so: liblapack.so.3
++	ln -sf $< $@ 
++
++liblapack.so.3: liblapack.so.3.0
++	ln -sf $< $@ 
++
++liblapack.so.3.0 : liblapack.a libatlas.so libcblas.so libf77blas.so
++	ld $(LDFLAGS) -shared -soname liblapack.so.3 -o $@ \
++	  --whole-archive liblapack.a  \
++	  --no-whole-archive -L. -lf77blas -lcblas -latlas -lm -lc $(F77SYSLIB)
++
++atlas/libblas.so: atlas/libblas.so.3
++	(cd atlas && ln -sf libblas.so.3 libblas.so)
++
++atlas/libblas.so.3: atlas/libblas.so.3.0
++	(cd atlas && ln -sf libblas.so.3.0 libblas.so.3)
++
++atlas/libblas.so.3.0: libf77blas.a libcblas.a libatlas.so.3.0
++	if test -f libptf77blas.a -a -f libptcblas.a; then \
++		ld $(LDFLAGS) -shared -soname libblas.so.3 -o $@ \
++		   --whole-archive libptf77blas.a libptcblas.a \
++	           --no-whole-archive -L. -latlas $(F77SYSLIB) -lm -lc; \
++	else \
++		ld $(LDFLAGS) -shared -soname libblas.so.3 -o $@ \
++		   --whole-archive libf77blas.a libcblas.a \
++	           --no-whole-archive -L. -latlas $(F77SYSLIB) -lm -lc; \
++	fi
++
++atlas/liblapack.so: atlas/liblapack.so.3
++	(cd atlas && ln -sf liblapack.so.3 liblapack.so)
++
++atlas/liblapack.so.3: atlas/liblapack.so.3.0
++	(cd atlas && ln -sf liblapack.so.3.0 liblapack.so.3)
++
++atlas/liblapack.so.3.0: atlas/liblapack.a atlas/libblas.so libatlas.so.3.0
++	ld $(LDFLAGS) -shared -soname liblapack.so.3 -o $@ \
++	   --whole-archive atlas/liblapack.a \
++           --no-whole-archive -L . -L atlas -lblas -latlas $(F77SYSLIB) -lm -lc
++
+ # ===================================================================
+ # The following commands are to build dynamic/shared objects on Linux
+ # using the gnu gcc or ld
+--- a/Make.top
++++ b/Make.top
+@@ -16,6 +16,7 @@ build:
+ 	cd bin/ ; ./xatlas_build $(INSTFLAGS)
+ 	cd lib/ ; $(MAKE) atlas/libblas.a
+ 	cd lib/ ; $(MAKE) atlas/liblapack.a
++	cd lib/ ; $(MAKE) fullshared
+ 
+ time: 
+ 	./xatlbench -dc $(BLDdir)/bin/INSTALL_LOG -dp $(BLDdir)/ARCHS/$(ARCH)
+@@ -683,3 +684,21 @@ install_static_lib:
+ 	- cp $(LIBdir)/libsatlas.so $(INSTdir)/.
+ 	- cp $(LIBdir)/libtatlas.so $(INSTdir)/.
+ 
++install_shared_lib:
++	for lib in atlas cblas f77blas lapack; do \
++		cp $(LIBdir)/lib$$lib.so.3.0 $(INSTdir)/. ; \
++		( cd $(INSTdir) && ln -s lib$$lib.so.3.0 lib$$lib.so.3); \
++		( cd $(INSTdir) && ln -s lib$$lib.so.3 lib$$lib.so); \
++		chmod 0644 $(INSTdir)/lib$$lib.so ;\
++		chmod 0644 $(INSTdir)/lib$$lib.so.3 ;\
++		chmod 0644 $(INSTdir)/lib$$lib.so.3.0 ;\
++	done;
++	mkdir -p $(INSTdir)/atlas
++	for lib in blas lapack; do \
++		cp $(LIBdir)/atlas/lib$$lib.so.3.0 $(INSTdir)/atlas/. ; \
++		( cd $(INSTdir)/atlas/ && ln -s lib$$lib.so.3.0 lib$$lib.so.3); \
++		( cd $(INSTdir)/atlas/ && ln -s lib$$lib.so.3 lib$$lib.so); \
++		chmod 0644 $(INSTdir)/atlas/lib$$lib.so ;\
++		chmod 0644 $(INSTdir)/atlas/lib$$lib.so.3 ;\
++		chmod 0644 $(INSTdir)/atlas/lib$$lib.so.3.0 ;\
++	done;
+--- a/CONFIG/src/Makefile
++++ b/CONFIG/src/Makefile
+@@ -576,6 +576,7 @@ $(LIBINSTdir) :
+ install : $(INCINSTdir) $(LIBINSTdir) $(INCINSTdir)/atlas
+ 	$(MAKE) -f Make.top install_inc INSTdir=$(INCINSTdir) 
+ 	$(MAKE) -f Make.top install_static_lib INSTdir=$(LIBINSTdir)
++	$(MAKE) -f Make.top install_shared_lib INSTdir=$(LIBINSTdir)
+ 
+ confclean: $(CLEANdep)
+ 	rm -f *core* *.o config?.out
diff --git a/atlas/default/static_full_blas_lapack.diff b/atlas/default/static_full_blas_lapack.diff
new file mode 100644
index 00000000..788be9bb
--- /dev/null
+++ b/atlas/default/static_full_blas_lapack.diff
@@ -0,0 +1,116 @@
+Description: Create full featured static libblas.a and liblapack.a
+ The resulting BLAS library will use the threaded flavour if the build has been
+ configured to create them. Otherwise, the serial library is used.
+Author: David Evans
+Last-Update: 2013-06-05
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- a/Make.top
++++ b/Make.top
+@@ -14,6 +14,9 @@
+ build:
+ 	cd bin/ ; $(MAKE) xatlas_build
+ 	cd bin/ ; ./xatlas_build $(INSTFLAGS)
++	cd lib/ ; $(MAKE) atlas/libblas.a
++	cd lib/ ; $(MAKE) atlas/liblapack.a
++
+ time: 
+ 	./xatlbench -dc $(BLDdir)/bin/INSTALL_LOG -dp $(BLDdir)/ARCHS/$(ARCH)
+ C_sanity_test:
+@@ -401,6 +404,7 @@
+ 	$(MAKE) -f Make.top leafstart leaf=src/blas/reference/level1
+ 	$(MAKE) -f Make.top leafstart leaf=src/auxil
+ 	$(MAKE) -f Make.top leafstart leaf=src/testing
++	$(MAKE) -f Make.top leafstart leaf=lib/atlas
+ 	$(MAKE) -f Make.top leafstart leaf=lib
+ 	$(MAKE) -f Make.top leafstart leaf=bin
+ 	cd src/threads ; touch atomic.inc
+@@ -591,6 +595,7 @@
+ 
+ lib :
+ 	mkdir lib
++	mkdir lib/atlas
+ 
+ include:
+ 	mkdir include
+@@ -654,12 +659,17 @@
+ 	chmod 0644 $(INSTdir)/cblas.h $(INSTdir)/clapack.h
+ 	cp $(INCAdir)/* $(INSTdir)/atlas/.
+ 	- chmod 0644 $(INSTdir)/atlas/*
+-install_lib:
++
++install_static_lib:
+ 	cp $(LIBdir)/libatlas.a $(INSTdir)/.
+ 	cp $(LIBdir)/libcblas.a $(INSTdir)/.
+ 	cp $(LIBdir)/liblapack.a $(INSTdir)/.
++	mkdir -p $(INSTdir)/atlas
++	cp $(LIBdir)/atlas/libblas.a $(INSTdir)/atlas/.
++	cp $(LIBdir)/atlas/liblapack.a $(INSTdir)/atlas/.
+ 	chmod 0644 $(INSTdir)/libatlas.a  $(INSTdir)/liblapack.a \
+-                   $(INSTdir)/libcblas.a 
++                   $(INSTdir)/libcblas.a $(INSTdir)/atlas/libblas.a \
++		   $(INSTdir)/atlas/liblapack.a 
+ 	- cp $(LIBdir)/libf77blas.a $(INSTdir)/.
+ 	- chmod 0644 $(INSTdir)/libf77blas.a
+ 	- cp $(LIBdir)/libptcblas.a $(INSTdir)/.
+--- a/makes/Make.lib
++++ b/makes/Make.lib
+@@ -175,6 +175,35 @@
+            LIBS="$(LIBS)" LIBINSTdir="$(LIBINSTdir)" ; \
+         fi
+ 
++
++# Build full netlib blas/lapack libraries:
++atlas/libblas.a: libatlas.a
++	mkdir tmp
++	cd tmp && \
++		ar x ../libatlas.a && \
++		if test -f ../libptf77blas.a -a -f ../libptcblas.a; then \
++			ar x ../libptf77blas.a && \
++			ar x ../libptcblas.a; \
++		else \
++			ar x ../libf77blas.a && \
++			ar x ../libcblas.a; \
++		fi
++	ar r $@ tmp/*.o
++	rm -rf tmp
++
++atlas/liblapack.a: liblapack.a libatlas.a
++	mkdir tmp
++	cd tmp && \
++		ar x ../liblapack.a && \
++		if test -f ../libptcblas.a; then \
++			ar x ../libptcblas.a; \
++		else \
++			ar x ../libcblas.a; \
++		fi
++	ar r $@ tmp/*.o
++	rm -rf tmp
++
++
+ #
+ # Builds one shared lib from all ATLAS files
+ #
+--- a/CONFIG/src/Makefile
++++ b/CONFIG/src/Makefile
+@@ -575,7 +575,7 @@
+ 	chmod 0755 $(LIBINSTdir)
+ install : $(INCINSTdir) $(LIBINSTdir) $(INCINSTdir)/atlas
+ 	$(MAKE) -f Make.top install_inc INSTdir=$(INCINSTdir) 
+-	$(MAKE) -f Make.top install_lib INSTdir=$(LIBINSTdir)
++	$(MAKE) -f Make.top install_static_lib INSTdir=$(LIBINSTdir)
+ 
+ confclean: $(CLEANdep)
+ 	rm -f *core* *.o config?.out
+--- a/CONFIG/src/SpewMakeInc.c
++++ b/CONFIG/src/SpewMakeInc.c
+@@ -604,6 +604,9 @@
+    }
+    fprintf(fpout, "   TESTlib = $(LIBdir)/libtstatlas.a\n\n");
+ 
++   fprintf(fpout, "   FULLBLASlib = $(LIBdir)/atlas/libblas.a\n");
++   fprintf(fpout, "   FULLLAPACKlib = $(LIBdir)/atlas/liblapack.a\n");
++
+    fprintf(fpout, "#  -------------------------------------------\n");
+    fprintf(fpout, "#  Upper bound on largest cache size, in bytes\n");
+    fprintf(fpout, "#  -------------------------------------------\n");
diff --git a/bcftools/1.2/build.yml b/bcftools/1.2/build.yml
new file mode 100644
index 00000000..8d514767
--- /dev/null
+++ b/bcftools/1.2/build.yml
@@ -0,0 +1,17 @@
+build:
+  commands:
+  - tar jxf bcftools-${version}.tar.bz2
+  - cd bcftools-${version}
+  - sed -i.bak 's#/usr/local#/build/dest#' Makefile
+  - make
+  - make install
+  - tar zcf /host/bcftools-${version}-Linux-x86_64.tar.gz -C /build/dest .
+  urls:
+  - https://github.com/samtools/bcftools/releases/download/${version}/bcftools-${version}.tar.bz2
+meta:
+  image: debian:squeeze
+  version: !!python/unicode '1.2'
+prebuild:
+  packages: 'libc6-dev zlib1g-dev
+
+    '
diff --git a/bcftools/default/build.yml b/bcftools/default/build.yml
new file mode 100644
index 00000000..cf81515d
--- /dev/null
+++ b/bcftools/default/build.yml
@@ -0,0 +1,16 @@
+meta:
+    image: 'debian:squeeze'
+    version: 1.2
+prebuild:
+    packages: |
+        libc6-dev zlib1g-dev
+build:
+    urls:
+        - https://github.com/samtools/bcftools/releases/download/${version}/bcftools-${version}.tar.bz2
+    commands:
+        - tar jxf bcftools-${version}.tar.bz2
+        - cd bcftools-${version}
+        - sed -i.bak 's#/usr/local#/build/dest#' Makefile
+        - make
+        - make install
+        - tar zcf /host/bcftools-${version}-Linux-x86_64.tar.gz -C /build/dest .
diff --git a/build-all.sh b/build-all.sh
new file mode 100755
index 00000000..8c87ccbf
--- /dev/null
+++ b/build-all.sh
@@ -0,0 +1,14 @@
+./build ubuntu atlas
+./build ubuntu bcftools
+./build ubuntu emboos
+./build ubuntu jellyfish
+./build ubuntu kraken
+./build ubuntu ngninx
+./build ubuntu openms
+./build ubuntu pkiss
+./build ubuntu rnashapes
+./build ubuntu samtools
+./build ubuntu tpp
+./build ubuntu ucsc
+
+python build.py --quiet tbl2asn
diff --git a/build.py b/build.py
new file mode 100644
index 00000000..33fce4f4
--- /dev/null
+++ b/build.py
@@ -0,0 +1,183 @@
+#!/usr/bin/env python
+import subprocess
+import shutil
+import re
+import yaml
+import sys
+import os
+import argparse
+
+
+def main(package, version='default', image=None, dryrun=False, clone=False, quiet=False):
+    parent_dir = os.path.dirname(os.path.abspath(__file__))
+    build_dir = os.path.join(parent_dir, package, version)
+    log_file = os.path.join(parent_dir, package, 'build.log')
+
+    _store_new_version = False
+    if not os.path.exists(build_dir):
+        if os.path.exists(os.path.join(parent_dir, package, 'default')):
+            build_dir = os.path.join(parent_dir, package, 'default')
+            # In this case it's an "unknown" version, so we'll just be friendly
+            # and serialize their yaml into a new versioned directory for them.
+            _store_new_version = True
+        else:
+            if version == 'default':
+                print "Default recipe for %s not found" % image
+            else:
+                print "Neither a default recipe, nor a recipe at version %s were found" % version
+            sys.exit(4)
+
+    if _store_new_version and clone:
+        target = os.path.join(parent_dir, package, version)
+        # Clone the default
+        shutil.copytree(build_dir, target)
+        # Update other variables.
+        build_dir = target
+
+    tentative_yaml_path = os.path.join(build_dir, 'build.yml')
+
+    if not os.path.exists(tentative_yaml_path) and not os.path.isdir(tentative_yaml_path):
+        print "No yaml file found at %s" % tentative_yaml_path
+        sys.exit(3)
+
+    with open(tentative_yaml_path, 'r') as handle:
+        image_data = yaml.load(handle)
+
+    DOCKER_TEMPLATE = """
+FROM %(image)s
+MAINTAINER Nare Coraor <nate@bx.psu.edu>
+
+ENV DEBIAN_FRONTEND noninteractive
+%(meta_env_string)s
+%(env_string)s
+
+VOLUME ["/host"]
+# Pre-build packages
+%(prebuild_packages)s
+
+# Pre-build commands
+%(prebuild_commands)s
+
+ENTRYPOINT ["/bin/bash", "/host/build.sh"]
+    """
+
+    SCRIPT_TEMPLATE = """#!/bin/sh
+urls="
+{url_list}
+"
+
+mkdir -p /build/ && cd /build/;
+
+( for url in $urls; do
+    wget --quiet "$url" || false || exit
+done)
+
+{commands}"""
+
+    template_values = {'image': 'ubuntu', 'prebuild_commands': "", 'env_string': ""}
+    # ENVIRONMENT
+    meta_env = {}
+    docker_env = {}
+    # If there's a 'meta' section, copy that into the environment, as we've
+    # stored things like OS/package name/version there historically. Useful now
+    # for the 'default' images which have a version hardcoded.
+    if 'meta' in image_data:
+        meta_env = image_data['meta']
+        template_values['image'] = image_data['meta'].get('image', 'ubuntu')
+
+    # If an image is sepecified, we overwrite the Dockerfile's FROM with that
+    # image
+    if image is not None:
+        template_values['image'] = image
+    # Additionally we store the actual image that the package is built with in
+    # the environment, so it's accessible to build scripts.
+    docker_env['image'] = template_values['image']
+
+    # The docker environment (in the Dockerfile) is built from the image_data's
+    # meta, and 'env' sections.
+    if 'env' in image_data:
+        docker_env.update(image_data['env'])
+    template_values['env_string'] = '\n'.join(['ENV %s %s' % (key, docker_env[key])
+                                               for key in docker_env])
+    template_values['meta_env_string'] = '\n'.join(['ENV %s %s' % (key, meta_env[key])
+                                                    for key in meta_env])
+
+    # Version is often used to construct downloads, if it's set to "default",
+    # then re-set it to the value in the default image's metadat
+    if version == 'default':
+        version = image_data['meta'].get('version', 'default')
+
+    prebuild_packages = ['wget', 'openssl', 'ca-certificates', 'build-essential']
+    if 'prebuild' in image_data and 'packages' in image_data['prebuild']:
+        pkgs = image_data['prebuild']['packages']
+        if isinstance(pkgs, str):
+            prebuild_packages.extend(pkgs.strip().split())
+        elif isinstance(pkgs, list):
+            prebuild_packages.extend(pkgs)
+        else:
+            print "Unknown data type for /prebuild/packages, please use a space delimited string of package names, or a list of strings"
+            sys.exit(5)
+
+    template_values['prebuild_packages'] = "RUN apt-get -qq update && apt-get install --no-install-recommends -y %s" % ' '.join(prebuild_packages)
+
+    if 'prebuild' in image_data and 'commands' in image_data['prebuild']:
+        template_values['prebuild_commands'] = '\n'.join([
+            'RUN %s' % command.strip()
+            for command in image_data['prebuild']['commands']
+        ])
+
+    with open(os.path.join(build_dir, 'Dockerfile'), 'w') as dockerfile:
+        dockerfile.write(DOCKER_TEMPLATE % template_values)
+
+    with open(os.path.join(build_dir, 'build.sh'), 'w') as script:
+        urls = image_data['build'].get('urls', [])
+        commands = image_data['build'].get('commands', [])
+
+        script.write(SCRIPT_TEMPLATE.format(url_list=' '.join(urls),
+                                            commands='\n'.join(commands)))
+
+    image_name = re.sub('[^A-Za-z0-9_]', '_', 'docker_build_%s_%s' % (package, template_values['image']))
+    command = ['docker', 'build', '-t', image_name, '.']
+    runcmd = ['docker', 'run', '--volume=%s/:/host/' % build_dir, '--env=pkg=%s' % package,
+              '--env=version=%s' % version, image_name]
+    if not dryrun:
+        with open(log_file, 'w') as handle:
+            execute(command, cwd=build_dir, log=handle, quiet=quiet)
+            if not quiet:
+                print ' '.join(runcmd)
+            execute(runcmd, cwd=build_dir, log=handle, quiet=quiet)
+    else:
+        # I am *lazy* during debugging phase
+        runcmd = runcmd[0:3] + ['-it', '--entrypoint=/bin/bash'] + runcmd[3:]
+        print ' '.join(command)
+        print ' '.join(runcmd)
+
+
+def execute(command, cwd=None, log=None, quiet=False):
+    popen = subprocess.Popen(command, stdout=subprocess.PIPE, cwd=cwd)
+    for line in iter(popen.stdout.readline, b""):
+        try:
+            # Log output on demand, rather than just stdout
+
+            # I don't know why I write these features when I only use them one
+            # way, and it's ugly, non-reusable code in the first place
+            if log is not None:
+                log.write(line)
+
+            if not quiet:
+                print line,
+        except KeyboardInterrupt:
+            sys.exit()
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Build things inside of docker')
+    parser.add_argument('package', help='Name of the package, should be a folder')
+    parser.add_argument('--version', help='Version of the package, should be a folder inside package, or "default" for versionless recipes',
+                        default='default')
+    parser.add_argument('--dryrun', action='store_true', help='Only generate files, does not build and run the image')
+    parser.add_argument('--image', help='Build image against a different target OS, e.g. "debian:squeeze"')
+    parser.add_argument('--clone', action='store_true', help='When building a default image with a different version, clone the build.yml and hardcode the version')
+    parser.add_argument('--quiet', action='store_true', help='Be a bit quieter')
+    args = parser.parse_args()
+    main(**vars(args))
diff --git a/emboss/6.6.0/build.yml b/emboss/6.6.0/build.yml
new file mode 100644
index 00000000..5456140e
--- /dev/null
+++ b/emboss/6.6.0/build.yml
@@ -0,0 +1,22 @@
+build:
+  commands:
+  - mkdir -p $HOME/bin/${arch}/ /build/dest/bin /build/dest/lib/
+  - tar xfz EMBOSS-${version}.tar.gz
+  - cd EMBOSS-${version}
+  - export ORIGIN='$ORIGIN'
+  - export LDFLAGS='-Wl,-rpath,$${ORIGIN}/../lib'
+  - ./configure --prefix /build/dest --without-x
+  - make
+  - make install
+  - tar zcf /host/${pkg}-${version}-Linux-${arch}.tar.gz -C /build/dest .
+  urls:
+  - ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${version}.tar.gz
+env:
+  arch: x86_64
+meta:
+  image: debian:squeeze
+  version: 6.6.0
+prebuild:
+  packages: 'libc6-dev zlib1g-dev libncurses5-dev
+
+    '
diff --git a/emboss/default/build.yml b/emboss/default/build.yml
new file mode 100644
index 00000000..d089c748
--- /dev/null
+++ b/emboss/default/build.yml
@@ -0,0 +1,21 @@
+meta:
+    image: 'debian:squeeze'
+    version: 6.6.0
+env:
+    arch: x86_64
+prebuild:
+    packages: |
+        libc6-dev zlib1g-dev libncurses5-dev
+build:
+    urls:
+        - ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${version}.tar.gz
+    commands:
+        - mkdir -p $HOME/bin/${arch}/ /build/dest/bin /build/dest/lib/
+        - tar xfz EMBOSS-${version}.tar.gz
+        - cd EMBOSS-${version}
+        - export ORIGIN='$ORIGIN'
+        - export LDFLAGS='-Wl,-rpath,$${ORIGIN}/../lib'
+        - ./configure --prefix /build/dest --without-x
+        - make
+        - make install
+        - tar zcf /host/${pkg}-${version}-Linux-${arch}.tar.gz -C /build/dest .
diff --git a/jellyfish/default/build.yml b/jellyfish/default/build.yml
new file mode 100644
index 00000000..6ae91c5c
--- /dev/null
+++ b/jellyfish/default/build.yml
@@ -0,0 +1,16 @@
+meta:
+    image: 'debian:squeeze'
+    version: 1.1.11
+prebuild:
+    packages: |
+        libc6-dev zlib1g-dev
+build:
+    urls:
+        - http://www.cbcb.umd.edu/software/jellyfish/jellyfish-${version}.tar.gz
+    commands:
+        - tar xfz jellyfish-${version}.tar.gz
+        - cd jellyfish-${version}
+        - ./configure --prefix=/build/dest
+        - make
+        - make install
+        - tar zcf /host/jellyfish-${version}-Linux-x86_64.tar.gz -C /build/dest .
diff --git a/kraken/default/build.yml b/kraken/default/build.yml
new file mode 100644
index 00000000..ad20ed7c
--- /dev/null
+++ b/kraken/default/build.yml
@@ -0,0 +1,15 @@
+meta:
+    image: 'ubuntu'
+    version: 0.10.5-beta
+prebuild:
+    packages: |
+        libc6-dev zlib1g-dev
+build:
+    urls:
+        - https://ccb.jhu.edu/software/kraken/dl/kraken-${version}.tgz
+    commands:
+        - tar xfz kraken-${version}.tar.gz
+        - cd kraken-${version}
+        - mkdir -p /build/dest/bin
+        - sh install_kraken.sh /build/dest/bin/
+        - tar zcf /host/kraken-${version}-Linux-x86_64.tar.gz -C /build/dest .
diff --git a/nginx/default/build.yml b/nginx/default/build.yml
new file mode 100644
index 00000000..baea8327
--- /dev/null
+++ b/nginx/default/build.yml
@@ -0,0 +1,39 @@
+meta:
+    image: 'ubuntu'
+    version: 1.4.6
+prebuild:
+    packages: |
+        git
+build:
+    commands:
+        - ubuntu_version=${nginx_version}-1ubuntu3.2
+        - ppa_version=${ubuntu_version}ppa1
+        - dch_message="Restore the nginx-upload module from 2.2 branch in Github, now compatible with nginx 1.4.x."
+        - DEBFULLNAME="Nathan Coraor"
+        - DEBEMAIL="nate@bx.psu.edu"
+        - export ubuntu_version ppa_version dch_message DEBEMAIL DEBFULLNAME
+        - build=/host/build.$(hostname)
+        - echo 'America/New_York' > /etc/timezone
+        - dpkg-reconfigure tzdata
+        - apt-get source $pkg
+        - |
+            git clone -b 2.2 \
+                --single-branch https://github.com/vkholodkov/nginx-upload-module.git/ \
+                nginx-${nginx_version}/debian/modules/nginx-upload
+        - upload_module_shortrev=$(git --git-dir=nginx-${nginx_version}/debian/modules/nginx-upload/.git rev-parse --short HEAD)
+        - rm -rf nginx/debian/modules/nginx-upload/.git
+        - |
+            sed -e '/^ #Removed as it no longer works with 1.3.x and above.$/d' \
+                -e 's/^ #\(nginx-upload\)$/ \1/' \
+                -e 's%^ #\( Homepage: https://github.com/vkholodkov/nginx-upload-module\)$% \1/tree/2.2%' \
+                -e "s/^ # Version: 2.2.0.*$/  Version: 2.2.1-${upload_module_shortrev}/" \
+                -i nginx-${nginx_version}/debian/modules/README.Modules-versions
+        - |
+            sed -e 's#\(^\t    --add-module=$(MODULESDIR)/nginx-upload-progress \\\)#\t    --add-module=$(MODULESDIR)/nginx-upload \\\n\1#' \
+                -i nginx-${nginx_version}/debian/rules
+        - cd nginx-${nginx_version}
+        - dch -v ${ppa_version} -D ${dch_dist} "${dch_message}"
+        - debuild -S -sd -us -uc
+        - echo "To sign: debsign -S ${pkg}_${ppa_version}_source.changes" &&
+        - echo "To push: dput ppa:natefoo/nginx ${pkg}_${ppa_version}_source.changes" &&
+        - echo "To push: dput ppa:galaxyproject/nginx ${pkg}_${ppa_version}_source.changes"
diff --git a/nginx/default/control.patch b/nginx/default/control.patch
new file mode 100644
index 00000000..d7271d7d
--- /dev/null
+++ b/nginx/default/control.patch
@@ -0,0 +1,316 @@
+--- debian/control.orig	2015-02-26 20:39:55.592321023 -0500
++++ debian/control	2015-02-26 21:48:02.044147424 -0500
+@@ -32,16 +32,24 @@
+ 
+ Package: nginx
+ Architecture: all
+-Depends: nginx-core   (>= ${source:Version}) |
+-         nginx-full   (>= ${source:Version}) |
+-         nginx-light  (>= ${source:Version}) |
+-         nginx-extras (>= ${source:Version}) |
+-         nginx-naxsi  (>= ${source:Version}) ,
+-         nginx-core   (<< ${source:Version}.1~) |
+-         nginx-full   (<< ${source:Version}.1~) |
+-         nginx-light  (<< ${source:Version}.1~) |
+-         nginx-extras (<< ${source:Version}.1~) |
+-         nginx-naxsi  (<< ${source:Version}.1~) ,
++Depends: nginx-core             (>= ${nginxSourceDebVersion}) |
++         nginx-full             (>= ${nginxSourceDebVersion}) |
++         nginx-light            (>= ${nginxSourceDebVersion}) |
++         nginx-extras           (>= ${nginxSourceDebVersion}) |
++         nginx-naxsi            (>= ${nginxSourceDebVersion}) |
++         nginx-core-upload      (>= ${source:Version}) |
++         nginx-full-upload      (>= ${source:Version}) |
++         nginx-light-upload     (>= ${source:Version}) |
++         nginx-extras-upload    (>= ${source:Version}) ,
++         nginx-core             (<< ${nginxSourceDebVersion}.1~) |
++         nginx-full             (<< ${nginxSourceDebVersion}.1~) |
++         nginx-light            (<< ${nginxSourceDebVersion}.1~) |
++         nginx-extras           (<< ${nginxSourceDebVersion}.1~) |
++         nginx-naxsi            (<< ${nginxSourceDebVersion}.1~) |
++         nginx-core-upload      (<< ${source:Version}.1~) |
++         nginx-full-upload      (<< ${source:Version}.1~) |
++         nginx-light-upload     (<< ${source:Version}.1~) |
++         nginx-extras-upload    (<< ${source:Version}.1~) ,
+          ${misc:Depends}
+ Description: small, powerful, scalable web/proxy server
+  Nginx ("engine X") is a high-performance web and reverse proxy server
+@@ -51,45 +59,16 @@
+  This is a dependency package to install either nginx-core (by default),
+  nginx-full, nginx-light, nginx-extras, or nginx-naxsi.
+ 
+-Package: nginx-doc
+-Architecture: all
+-Section: doc
+-Depends: lsb-base (>= 3.2-14), ${misc:Depends}
+-Description: small, powerful, scalable web/proxy server - documentation
+- Nginx ("engine X") is a high-performance web and reverse proxy server
+- created by Igor Sysoev. It can be used both as a standalone web server
+- and as a proxy to reduce the load on back-end HTTP or mail servers.
+- .
+- This package provides extra documentation to help unleash the power of Nginx.
+-
+-Package: nginx-common
+-Architecture: all
+-Depends: lsb-base (>= 3.2-14), ${misc:Depends}
+-Replaces: nginx (<< 0.8.54-4),
+-          nginx-extras (<< 0.8.54-4),
+-          nginx-full (<< 0.8.54-4),
+-          nginx-light (<< 0.8.54-4)
+-Breaks: nginx (<< 0.8.54-4),
+-        nginx-extras (<< 0.8.54-4),
+-        nginx-full (<< 0.8.54-4),
+-        nginx-light (<< 0.8.54-4)
+-Suggests: fcgiwrap, nginx-doc
+-Description: small, powerful, scalable web/proxy server - common files
+- Nginx ("engine X") is a high-performance web and reverse proxy server
+- created by Igor Sysoev. It can be used both as a standalone web server
+- and as a proxy to reduce the load on back-end HTTP or mail servers.
+- .
+- This package contains base configuration files used by all versions of
+- nginx.
+-
+-Package: nginx-core
++Package: nginx-core-upload
+ Architecture: any
+-Depends: nginx-common (= ${source:Version}), ${misc:Depends}, ${shlibs:Depends}
++Depends: nginx-common (= ${nginxSourceDebVersion}), ${misc:Depends}, ${shlibs:Depends}
+ Breaks: nginx (<< 1.4.5-1)
+ Provides: httpd, httpd-cgi, nginx
+-Conflicts: nginx-extras, nginx-light, nginx-naxsi, nginx-full
+-Suggests: nginx-doc (= ${source:Version})
+-Description: nginx web/proxy server (core version)
++Conflicts: nginx-extras, nginx-light, nginx-naxsi, nginx-full,
++           nginx-extras-upload, nginx-light-upload,
++           nginx-full-upload
++Suggests: nginx-doc (= ${nginxSourceDebVersion})
++Description: nginx web/proxy server (core+upload version)
+  Nginx ("engine X") is a high-performance web and reverse proxy server
+  created by Igor Sysoev. It can be used both as a standalone web server
+  and as a proxy to reduce the load on back-end HTTP or mail servers.
+@@ -109,16 +88,20 @@
+  .
+  MAIL MODULES: Mail Core, IMAP, POP3, SMTP, SSL.
+  .
+- NOTE: This is identical to the -full build, but without any third party
+- modules built in.
++ THIRD PARTY MODULES: Upload.
++ .
++ NOTE: This is identical to the -full build, but with only the upload third
++ party module built in.
+ 
+-Package: nginx-core-dbg
++Package: nginx-core-upload-dbg
+ Architecture: any
+ Section: debug
+ Priority: extra
+-Depends: nginx-core (= ${binary:Version}), ${misc:Depends}
+-Conflicts: nginx-extras-dbg, nginx-light-dbg, nginx-naxsi-dbg, nginx-full-dbg
+-Description: nginx web/proxy server (core version) - debugging symbols
++Depends: nginx-core-upload (= ${binary:Version}), ${misc:Depends}
++Conflicts: nginx-extras-dbg, nginx-light-dbg, nginx-naxsi-dbg, nginx-full-dbg,
++           nginx-extras-upload-dbg, nginx-light-upload-dbg,
++           nginx-full-upload-dbg
++Description: nginx web/proxy server (core+upload version) - debugging symbols
+  Nginx ("engine X") is a high-performance web and reverse proxy server
+  created by Igor Sysoev. It can be used both as a standalone web server
+  and as a proxy to reduce the load on back-end HTTP or mail servers.
+@@ -126,14 +109,15 @@
+  This package provides debugging symbols for nginx-core, to assist in debugging
+  issues that you may find. It should not be required for normal operation.
+ 
+-Package: nginx-full
++Package: nginx-full-upload
+ Architecture: any
+-Depends: nginx-common (= ${source:Version}), ${misc:Depends}, ${shlibs:Depends}
++Depends: nginx-common (= ${nginxSourceDebVersion}), ${misc:Depends}, ${shlibs:Depends}
+ Breaks: nginx (<< 1.4.5-1)
+ Provides: httpd, httpd-cgi, nginx
+-Conflicts: nginx-extras, nginx-light, nginx-naxsi, nginx-core
+-Suggests: nginx-doc (= ${source:Version})
+-Description: nginx web/proxy server (standard version)
++Conflicts: nginx-extras, nginx-light, nginx-naxsi, nginx-core,
++           nginx-extras-upload, nginx-light-upload, nginx-core-upload
++Suggests: nginx-doc (= ${nginxSourceDebVersion})
++Description: nginx web/proxy server (standard+upload version)
+  Nginx ("engine X") is a high-performance web and reverse proxy server
+  created by Igor Sysoev. It can be used both as a standalone web server
+  and as a proxy to reduce the load on back-end HTTP or mail servers.
+@@ -154,15 +138,17 @@
+  MAIL MODULES: Mail Core, IMAP, POP3, SMTP, SSL.
+  .
+  THIRD PARTY MODULES: Auth PAM, DAV Ext, Echo, HTTP Substitution Filter,
+- Upstream Fair Queue.
++ Upstream Fair Queue, Upload.
+ 
+-Package: nginx-full-dbg
++Package: nginx-full-upload-dbg
+ Architecture: any
+ Section: debug
+ Priority: extra
+-Depends: nginx-full (= ${binary:Version}), ${misc:Depends}
+-Conflicts: nginx-extras-dbg, nginx-light-dbg, nginx-naxsi-dbg, nginx-core-dbg
+-Description: nginx web/proxy server (standard version) - debugging symbols
++Depends: nginx-full-upload (= ${binary:Version}), ${misc:Depends}
++Conflicts: nginx-extras-dbg, nginx-light-dbg, nginx-naxsi-dbg, nginx-core-dbg,
++           nginx-extras-upload-dbg, nginx-light-upload-dbg,
++           nginx-core-upload-dbg
++Description: nginx web/proxy server (standard+upload version) - debugging symbols
+  Nginx ("engine X") is a high-performance web and reverse proxy server
+  created by Igor Sysoev. It can be used both as a standalone web server
+  and as a proxy to reduce the load on back-end HTTP or mail servers.
+@@ -170,15 +156,16 @@
+  This package provides debugging symbols for nginx-full, to assist in debugging
+  issues that you may find. It should not be required for normal operation.
+ 
+-Package: nginx-light
++Package: nginx-light-upload
+ Architecture: any
+ Priority: extra
+-Depends: nginx-common (= ${source:Version}), ${misc:Depends}, ${shlibs:Depends}
++Depends: nginx-common (= ${nginxSourceDebVersion}), ${misc:Depends}, ${shlibs:Depends}
+ Breaks: nginx (<< 1.4.5-1)
+ Provides: httpd, httpd-cgi, nginx
+-Conflicts: nginx-extras, nginx-full, nginx-naxsi, nginx-core
+-Suggests: nginx-doc (= ${source:Version})
+-Description: nginx web/proxy server (basic version)
++Conflicts: nginx-extras, nginx-full, nginx-naxsi, nginx-core,
++           nginx-extras-upload, nginx-full-upload, nginx-core-upload
++Suggests: nginx-doc (= ${nginxSourceDebVersion})
++Description: nginx web/proxy server (basic+upload version)
+  Nginx ("engine X") is a high-performance web and reverse proxy server
+  created by Igor Sysoev. It can be used both as a standalone web server
+  and as a proxy to reduce the load on back-end HTTP or mail servers.
+@@ -192,15 +179,17 @@
+  OPTIONAL HTTP MODULES: Debug, Gzip Precompression, IPv6, Real Ip, SSL,
+  Stub Status.
+  .
+- THIRD PARTY MODULES: Echo.
++ THIRD PARTY MODULES: Echo, Upload.
+ 
+-Package: nginx-light-dbg
++Package: nginx-light-upload-dbg
+ Architecture: any
+ Section: debug
+ Priority: extra
+-Depends: nginx-light (= ${binary:Version}), ${misc:Depends}
+-Conflicts: nginx-extras-dbg, nginx-full-dbg, nginx-naxsi-dbg, nginx-core-dbg
+-Description: nginx web/proxy server (basic version) - debugging symbols
++Depends: nginx-light-upload (= ${binary:Version}), ${misc:Depends}
++Conflicts: nginx-extras-dbg, nginx-full-dbg, nginx-naxsi-dbg, nginx-core-dbg,
++           nginx-extras-upload-dbg, nginx-full-upload-dbg,
++           nginx-core-upload-dbg
++Description: nginx web/proxy server (basic+upload version) - debugging symbols
+  Nginx ("engine X") is a high-performance web and reverse proxy server
+  created by Igor Sysoev. It can be used both as a standalone web server
+  and as a proxy to reduce the load on back-end HTTP or mail servers.
+@@ -209,18 +198,19 @@
+  debugging issues that you may find. It should not be required for normal
+  operation.
+ 
+-Package: nginx-extras
++Package: nginx-extras-upload
+ Architecture: any
+ Priority: extra
+-Depends: nginx-common (= ${source:Version}),
++Depends: nginx-common (= ${nginxSourceDebVersion}),
+          ${misc:Depends},
+          ${perl:Depends},
+          ${shlibs:Depends}
+ Breaks: nginx (<< 1.4.5-1)
+ Provides: httpd, httpd-cgi, nginx
+-Conflicts: nginx-full, nginx-light, nginx-naxsi, nginx-core
+-Suggests: nginx-doc (= ${source:Version})
+-Description: nginx web/proxy server (extended version)
++Conflicts: nginx-full, nginx-light, nginx-naxsi, nginx-core,
++           nginx-full-upload, nginx-light-upload, nginx-core-upload
++Suggests: nginx-doc (= ${nginxSourceDebVersion})
++Description: nginx web/proxy server (extended+upload version)
+  Nginx ("engine X") is a high-performance web and reverse proxy server
+  created by Igor Sysoev. It can be used both as a standalone web server
+  and as a proxy to reduce the load on back-end HTTP or mail servers.
+@@ -242,15 +232,15 @@
+  .
+  THIRD PARTY MODULES: Auth PAM, Chunkin, DAV Ext, Echo, Embedded Lua,
+  Fancy Index, HttpHeadersMore, HTTP Substitution Filter, http push,
+- Nginx Development Kit, Upload Progress, Upstream Fair Queue.
++ Nginx Development Kit, Upload Progress, Upstream Fair Queue, Upload.
+ 
+-Package: nginx-extras-dbg
++Package: nginx-extras-upload-dbg
+ Architecture: any
+ Section: debug
+ Priority: extra
+-Depends: nginx-extras (= ${binary:Version}), ${misc:Depends}
++Depends: nginx-extras-upload (= ${binary:Version}), ${misc:Depends}
+ Conflicts: nginx-full-dbg, nginx-light-dbg, nginx-naxsi-dbg, nginx-core-dbg
+-Description: nginx web/proxy server (extended version) - debugging symbols
++Description: nginx web/proxy server (extended+upload version) - debugging symbols
+  Nginx ("engine X") is a high-performance web and reverse proxy server
+  created by Igor Sysoev. It can be used both as a standalone web server
+  and as a proxy to reduce the load on back-end HTTP or mail servers.
+@@ -258,64 +248,3 @@
+  This package provides debugging symbols for nginx-extras, to assist in
+  debugging issues that you may find. It should not be required for normal
+  operation.
+-
+-Package: nginx-naxsi
+-Architecture: any
+-Priority: extra
+-Depends: nginx-common (= ${source:Version}), ${misc:Depends}, ${shlibs:Depends}
+-Breaks: nginx (<< 1.4.5-1),
+-        nginx-naxsi-ui (<< 1.4.5-1)
+-Provides: httpd, httpd-cgi, nginx
+-Conflicts: nginx-extras, nginx-full, nginx-light, nginx-core
+-Description: nginx web/proxy server (version with naxsi)
+- Nginx ("engine X") is a high-performance web and reverse proxy server
+- created by Igor Sysoev. It can be used both as a standalone web server
+- and as a proxy to reduce the load on back-end HTTP or mail servers.
+- .
+- This package provides a version of nginx with the basic modules, plus
+- the naxsi Web Application Firewall module.
+- .
+- STANDARD HTTP MODULES: Core, Access, Auth Basic, Auto Index, Browser,
+- Charset, Core, Empty GIF, FastCGI, Geo, Gzip, Headers, Index,
+- Limit Requests, Limit Zone, Log, Map, Memcached, Proxy, Referer,
+- Rewrite, Split Clients, SSI, Upstream, User ID.
+- .
+- OPTIONAL HTTP MODULES: Debug, IPv6, Real IP, SSL, Stub Status.
+- .
+- THIRD PARTY MODULES: Naxsi, Cache Purge, Upstream Fair.
+-
+-Package: nginx-naxsi-dbg
+-Architecture: any
+-Section: debug
+-Priority: extra
+-Depends: nginx-naxsi (= ${binary:Version}), ${misc:Depends}
+-Conflicts: nginx-extras-dbg, nginx-full-dbg, nginx-light-dbg, nginx-core-dbg
+-Description: nginx web/proxy server (version with naxsi) - debugging symbols
+- Nginx ("engine X") is a high-performance web and reverse proxy server
+- created by Igor Sysoev. It can be used both as a standalone web server
+- and as a proxy to reduce the load on back-end HTTP or mail servers.
+- .
+- This package provides debugging symbols for nginx-naxsi, to assist in
+- debugging issues that you may find. It should not be required for normal
+- operation.
+-
+-Package: nginx-naxsi-ui
+-Architecture: all
+-Priority: extra
+-Depends: daemon,
+-         dbconfig-common,
+-         nginx-naxsi (>= ${source:Version}),
+-         nginx-naxsi (<< ${source:Version}.1~),
+-         python-twisted-web,
+-         ${misc:Depends}
+-Description: nginx web/proxy server - naxsi configuration front-end
+- Nginx ("engine X") is a high-performance web and reverse proxy server
+- created by Igor Sysoev. It can be used both as a standalone web server
+- and as a proxy to reduce the load on back-end HTTP or mail servers.
+- .
+- This package provides the autolearning daemon and web user interface for
+- nginx's naxsi module.
+- .
+- It includes an interceptor (listening on TCP port 8080), which monitors
+- HTTP requests from naxsi, and an extractor (running on TCP port 8081),
+- which reads the database and prints reports about blocked requests.
diff --git a/nginx/default/rules.patch b/nginx/default/rules.patch
new file mode 100644
index 00000000..eb5ac8f2
--- /dev/null
+++ b/nginx/default/rules.patch
@@ -0,0 +1,119 @@
+--- debian/rules.orig	2015-02-26 19:58:46.218909084 -0500
++++ debian/rules	2015-02-26 22:13:48.193023932 -0500
+@@ -2,19 +2,19 @@
+ 
+ debian_cflags:=$(shell dpkg-buildflags --get CFLAGS | sed 's/-O3/-O2/') $(shell dpkg-buildflags --get CPPFLAGS)
+ debian_ldflags:=$(shell dpkg-buildflags --get LDFLAGS)
++nginxSourceDebVersion:=$(shell cat debian/nginxSourceDebVersion)
+ 
+ # export necessary for (hardening) flags for perl
+ # (src/http/modules/perl/Makefile.PL).
+ DEBIAN_NGINX_PERL_LDFLAGS:= $(debian_ldflags)
+ export DEBIAN_NGINX_PERL_LDFLAGS
+ 
+-FLAVOURS:=core full light extras naxsi
++FLAVOURS:=core-upload full-upload light-upload extras-upload
+ 
+-BUILDDIR_core = $(CURDIR)/debian/build-core
+-BUILDDIR_full = $(CURDIR)/debian/build-full
+-BUILDDIR_light = $(CURDIR)/debian/build-light
+-BUILDDIR_extras = $(CURDIR)/debian/build-extras
+-BUILDDIR_naxsi = $(CURDIR)/debian/build-naxsi
++BUILDDIR_core-upload = $(CURDIR)/debian/build-core-upload
++BUILDDIR_full-upload = $(CURDIR)/debian/build-full-upload
++BUILDDIR_light-upload = $(CURDIR)/debian/build-light-upload
++BUILDDIR_extras-upload = $(CURDIR)/debian/build-extras-upload
+ MODULESDIR = $(CURDIR)/debian/modules
+ BASEDIR = $(CURDIR)
+ 
+@@ -53,6 +53,7 @@
+ 			--with-http_ssl_module \
+ 			--with-http_stub_status_module \
+ 			--with-http_realip_module \
++	    	--add-module=$(MODULESDIR)/nginx-upload \
+ 
+ config.env.%:
+ 	dh_testdir
+@@ -64,8 +65,8 @@
+ 	cp -Pa $(CURDIR)/src $(BUILDDIR_$*)/
+ 	cp -Pa $(CURDIR)/man $(BUILDDIR_$*)/
+ 
+-config.status.core: config.env.core
+-	cd $(BUILDDIR_core) && ./configure  \
++config.status.core-upload: config.env.core-upload
++	cd $(BUILDDIR_core-upload) && ./configure  \
+ 	    $(common_configure_flags) \
+ 	    --with-http_addition_module \
+ 	    --with-http_dav_module \
+@@ -80,8 +81,8 @@
+             >$@
+ 	touch $@
+ 
+-config.status.full: config.env.full
+-	cd $(BUILDDIR_full) && ./configure  \
++config.status.full-upload: config.env.full-upload
++	cd $(BUILDDIR_full-upload) && ./configure  \
+ 	    $(common_configure_flags) \
+ 	    --with-http_addition_module \
+ 	    --with-http_dav_module \
+@@ -101,8 +102,8 @@
+             >$@
+ 	touch $@
+ 
+-config.status.light: config.env.light
+-	cd $(BUILDDIR_light) && ./configure  \
++config.status.light-upload: config.env.light-upload
++	cd $(BUILDDIR_light-upload) && ./configure  \
+ 	    $(common_configure_flags) \
+ 	    --with-http_gzip_static_module \
+ 	    --without-http_browser_module \
+@@ -120,8 +121,8 @@
+             >$@
+ 	touch $@
+ 
+-config.status.extras: config.env.extras
+-	cd $(BUILDDIR_extras) && ./configure  \
++config.status.extras-upload: config.env.extras-upload
++	cd $(BUILDDIR_extras-upload) && ./configure  \
+ 	    $(common_configure_flags) \
+ 	    --with-http_addition_module \
+ 	    --with-http_dav_module \
+@@ -153,20 +154,6 @@
+             >$@
+ 	touch $@
+ 
+-config.status.naxsi: config.env.naxsi
+-	cd $(BUILDDIR_naxsi) && ./configure  \
+-	    $(common_configure_flags) \
+-	    --without-mail_pop3_module \
+-	    --without-mail_smtp_module \
+-	    --without-mail_imap_module \
+-	    --without-http_uwsgi_module \
+-	    --without-http_scgi_module \
+-	    --add-module=$(MODULESDIR)/naxsi/naxsi_src \
+-	    --add-module=$(MODULESDIR)/nginx-cache-purge \
+-	    --add-module=$(MODULESDIR)/nginx-upstream-fair \
+-	    >$@
+-	touch $@
+-
+ config.status.%:
+ 	echo "configuration for flavour $* not yet defined."
+ 
+@@ -223,7 +210,7 @@
+ 	dh_compress -i
+ 	dh_fixperms -i
+ 	dh_installdeb -i
+-	dh_gencontrol -i
++	dh_gencontrol -i -- -VnginxSourceDebVersion=$(nginxSourceDebVersion)
+ 	dh_md5sums -i
+ 	dh_builddeb -i
+ 
+@@ -239,7 +226,7 @@
+ 	dh_fixperms -a
+ 	dh_installdeb -a
+ 	dh_shlibdeps -a
+-	dh_gencontrol -a
++	dh_gencontrol -a -- -VnginxSourceDebVersion=$(nginxSourceDebVersion)
+ 	dh_md5sums -a
+ 	dh_builddeb -a
+ 
diff --git a/openms/default/build.yml b/openms/default/build.yml
new file mode 100644
index 00000000..efc2bda5
--- /dev/null
+++ b/openms/default/build.yml
@@ -0,0 +1,49 @@
+meta:
+    image: 'debian:squeeze'
+    version: master
+prebuild:
+    packages: |
+        libc6-dev zlib1g-dev libncurses5-dev libtool libqt4-dev libbz2-dev
+        cmake autoconf automake
+    commands:
+        # Unfortunately this executes after packges :|
+        # TODO: refactor prebuild a list of dicts with a
+        # 'type=package|command'
+        - echo 'deb http://http.debian.net/debian-backports squeeze-backports main' >> /etc/apt/sources.list
+build:
+    urls:
+        - https://github.com/OpenMS/OpenMS/archive/Release2.0.0.tar.gz
+        - https://github.com/OpenMS/contrib/archive/master.tar.gz
+    commands:
+        # Since a newer version of cmake is required...we update it now.
+        - apt-get -qq update && apt-get dist-upgrade -y
+        - mkdir -p /build/dest/bin /build/dest/lib /usr/lib/x86_64-linux-gnu/libgthread-2.0.so
+        - tar xfz Release2.0.0.tar.gz
+        - tar xfz master.tar.gz
+        - mv contrib-master OpenMS-Release2.0.0/contrib
+        - cd OpenMS-Release2.0.0/contrib
+        - cmake . -DBUILD_TYPE=SEQAN
+        - cmake . -DBUILD_TYPE=LIBSVM
+        - cmake . -DBUILD_TYPE=XERCESC
+        - cmake . -DBUILD_TYPE=GSL
+        - cmake . -DBUILD_TYPE=BOOST -DNUMBER_OF_JOBS=4
+        - cmake . -DBUILD_TYPE=COINOR
+        - cmake . -DBUILD_TYPE=BZIP2
+        - cmake . -DBUILD_TYPE=GLPK
+        - cmake . -DBUILD_TYPE=EIGEN
+        - cmake . -DBUILD_TYPE=WILDMAGIC
+        - cd ..
+        - mkdir build 
+        - cd build
+        - ORIGIN='$ORIGIN'
+        - export ORIGIN
+        - LDFLAGS='-Wl,-rpath,$${ORIGIN}/../lib' cmake .. -DCMAKE_INSTALL_PREFIX=/build/dest -DHAS_XSERVER=OFF -DENABLE_TUTORIALS=OFF -DENABLE_STYLE_TESTING=OFF -DENABLE_UNITYBUILD=OFF -DWITH_GUI=OFF
+        - make OpenMS TOPP UTILS
+        - make install
+        - cp -d /usr/lib/libQtCore* /build/dest/lib/
+        - cp -d /usr/lib/libQtNetwork* /build/dest/lib/
+        - cp -d /usr/lib/libgomp.* /build/dest/lib/
+        - cp -d /lib/libglib-2.0* /build/dest/lib/
+        - cp -d /usr/lib/libgthread-2.0.so* /build/dest/lib/
+        - cp -d /lib/libpcre.so* /build/dest/lib/
+        - tar zcf /host/${pkg}-${version}-Linux-${arch}.tar.gz -C /build/dest .
diff --git a/perlgd/default/build.yml b/perlgd/default/build.yml
new file mode 100644
index 00000000..038093e4
--- /dev/null
+++ b/perlgd/default/build.yml
@@ -0,0 +1,10 @@
+meta:
+    image: 'debian:latest'
+    version: 2.56
+build:
+    urls:
+        - https://cpan.metacpan.org/authors/id/L/LD/LDS/GD-${version}.tar.gz
+    commands:
+        - tar xfz GD-${version}.tar.gz
+        - chmod ugo+w GD-${version}/bdf_scripts/*
+        - tar zcf /host/GD-${version}.tar.gz GD-${version}/
diff --git a/pkiss/default/build.yml b/pkiss/default/build.yml
new file mode 100644
index 00000000..9571c536
--- /dev/null
+++ b/pkiss/default/build.yml
@@ -0,0 +1,33 @@
+meta:
+    image: 'debian:squeeze'
+    version: 2.2.12
+prebuild:
+    packages: |
+        libboost-dev libboost-test-dev libboost-program-options-dev bison flex
+        mercurial ksh
+build:
+    urls:
+        - https://launchpad.net/~bibi-help/+archive/ubuntu/bibitools/+files/bellmansgapc_2015.03.17.orig.tar.gz
+        - https://launchpad.net/~bibi-help/+archive/ubuntu/bibitools/+files/pkiss_${version}.orig.tar.gz
+    commands:
+        - mkdir -p /build/dest/bin
+        - mkdir -p /build/dest/lib
+        - tar -xf bellmansgapc_2015.03.17.orig.tar.gz
+        - tar -xf pkiss_${version}.orig.tar.gz
+        - cd bellmansgapc-2015.03.17
+        - cp config-templates/generic.mf config.mf
+        - sed -i 's|#PREFIX ?=|PREFIX = /build/gapc|g' config.mf
+        - make
+        - make install
+        - cp -r /build/gapc/lib /build/dest
+        - export PATH=$PATH:/build/gapc/bin
+        - cd ../pkiss_2.2.12/pkiss
+        - make -C Misc/Applications/pKiss all 
+        - cp -r Misc/Applications/lib/* /build/dest/lib
+        - cp Misc/Applications/pKiss/x86_64-linux-gnu/* /build/dest/bin
+        - cp Misc/Applications/pKiss/pKiss /build/dest/bin
+        # for the librna.so and librnafast.so
+        # export LD_LIBRARY_PATH=installdir/lib:$LD_LIBRARY_PATH
+        # for the binaries
+        # export PATH=installdir/bin:$PATH
+        - tar zcf /host/${pkg}-${version}-Linux-${arch}.tar.gz -C /build/dest .
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 00000000..c83b3ed2
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,3 @@
+pyyaml
+beautifulsoup4
+filecache
diff --git a/samtools/default/build.yml b/samtools/default/build.yml
new file mode 100644
index 00000000..0697c506
--- /dev/null
+++ b/samtools/default/build.yml
@@ -0,0 +1,19 @@
+meta:
+    image: 'debian:squeeze'
+    version: 0.1.19
+prebuild:
+    packages: |
+        libc6-dev zlib1g-dev libncurses5-dev
+build:
+    urls:
+        - http://downloads.sourceforge.net/project/samtools/samtools/${version}/samtools-${version}.tar.bz2
+    commands:
+        - tar jxf samtools-${version}.tar.bz2
+        - cd samtools-${version}
+        - make
+        - mkdir -p /build/dest/bin /build/dest/lib /build/dest/include/bam /build/dest/include/bcf
+        - cp samtools bcftools/bcftools bcftools/vcfutils.pl /build/dest/bin
+        - cp libbam.a bcftools/libbcf.a /build/dest/lib
+        - cp *.h /build/dest/include/bam
+        - cp bcftools/*.h /build/dest/include/bcf
+        - tar zcf /host/samtools-${version}-Linux-x86_64.tar.gz -C /build/dest .
diff --git a/tbl2asn/default/build.yml b/tbl2asn/default/build.yml
new file mode 100644
index 00000000..854994f4
--- /dev/null
+++ b/tbl2asn/default/build.yml
@@ -0,0 +1,21 @@
+meta:
+    image: 'ubuntu'
+    pkg: tbl2asn
+prebuild:
+    packages: wget
+build:
+    urls:
+        # I'm not convinced that these will all be at the same version # but....well...there's not a lot to do.
+        - ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux.tbl2asn.gz
+        - ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz
+        - ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/mac.tbl2asn.gz
+        - ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/win.tbl2asn.zip
+    commands:
+        - gunzip linux64.tbl2asn.gz
+        - chmod +x linux64.tbl2asn
+        - version=$(./linux64.tbl2asn p | egrep 'tbl2asn ([^ ]*)' -o | sed 's/tbl2asn //g')
+        - gzip linux64.tbl2asn
+        - mv linux.tbl2asn.gz   /host/tbl2asn-${version}-Linux-x86.gz
+        - mv linux64.tbl2asn.gz /host/tbl2asn-${version}-Linux-x64.gz
+        - mv mac.tbl2asn.gz     /host/tbl2asn-${version}-Darwin-x64.gz
+        - mv win.tbl2asn.zip    /host/tbl2asn-${version}-Windows-x64.zip
diff --git a/tpp/default/build.yml b/tpp/default/build.yml
new file mode 100644
index 00000000..d6c48ab4
--- /dev/null
+++ b/tpp/default/build.yml
@@ -0,0 +1,29 @@
+meta:
+    image: 'debian:squeeze'
+    version: 4.8.0
+env:
+    arch: x86_64
+prebuild:
+    packages: |
+        libc6-dev zlib1g-dev libncurses5-dev libbz2-dev time libxml-parser-perl
+        libgd2-xpm-dev
+build:
+    urls:
+        - http://downloads.sourceforge.net/project/sashimi/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v4.8%20%28philae%29%20rev%200/TPP_${version}-src.tgz
+    commands:
+        - export build_dir=/build/dest/
+        - mkdir -p ${build_dir}/bin ${build_dir}/lib
+        - tar xfz TPP_${version}-src.tgz
+        - cd TPP-${version}/trans_proteomic_pipeline/src/
+        - echo "TPP_ROOT=${build_dir}" > Makefile.config.incl
+        - echo "TPP_WEB=${build_dir}/web/" >> Makefile.config.incl
+        - echo "CGI_USER_DIR=${build_dir}/cgi-bin/" >> Makefile.config.incl
+        - echo "HTMLDOC_BIN=" >> Makefile.config.incl
+        - echo "LINK=shared" >> Makefile.config.incl
+        - echo "LIBEXT=a" >> Makefile.config.incl
+        - make ARCH=linux-${arch} && make install ARCH=linux-${arch}
+        - cp /lib/libbz2.so.1.0.4 /build/dest/lib
+        - cd /build/dest/lib/
+        - ln -s ./libbz2.so.1.0.4 ./libbz2.so
+        - ln -s ./libbz2.so.1.0.4 ./libbz2.so.1.0
+        - tar zcf /host/${pkg}-${version}-Linux-${arch}.tar.gz -C /build/dest .
diff --git a/ucsc/314/build.yml b/ucsc/314/build.yml
new file mode 100644
index 00000000..9e3255e0
--- /dev/null
+++ b/ucsc/314/build.yml
@@ -0,0 +1,31 @@
+build:
+  commands:
+  - mkdir -p $HOME/bin/${arch}/ /build/dest/bin /build/dest/lib
+  - unzip jksrc.v${version}.zip
+  - cd kent/src/lib/
+  - make
+  - cd ../utils/
+  - COPT='-O -g -Wl,-rpath,$${ORIGIN}/../lib'
+  - ORIGIN='$ORIGIN'
+  - export COPT ORIGIN
+  - find . -type d -maxdepth 1 -mindepth 1 -exec make -C '{}' \;
+  - mv $HOME/bin/${arch}/* /build/dest/bin/
+  - "for lib in $(ldd /build/dest/bin/faToTwoBit | grep -o '=> /[^ ]*' | sed 's/=>\
+    \ //g'); \ndo\n    case $lib in\n        */libcrypto.so*|*/libgcc_s.so*|*/libmysqlclient.so*|*/libssl.so*|*/libstdc++.so*)\n\
+    \            echo \"including $lib\";\n            cp $lib /build/dest/lib/;\n\
+    \            ;;\n    esac\ndone\n"
+  - tar zcf /host/${pkg}-${version}-Linux-${arch}.tar.gz -C /build/dest .
+  urls:
+  - http://hgdownload.soe.ucsc.edu/admin/jksrc.v${version}.zip
+env:
+  arch: x86_64
+meta:
+  image: ubuntu
+  pkg: ucsc
+  version: '314'
+prebuild:
+  packages: 'libc6-dev zlib1g-dev libncurses5-dev libmysqlclient-dev unzip
+
+    libpng-dev libssl-dev
+
+    '
diff --git a/ucsc/default/build.yml b/ucsc/default/build.yml
new file mode 100644
index 00000000..f1bc44ce
--- /dev/null
+++ b/ucsc/default/build.yml
@@ -0,0 +1,35 @@
+meta:
+    image: 'ubuntu'
+    pkg: ucsc
+    version: 312
+env:
+    arch: x86_64
+prebuild:
+    packages: |
+        libc6-dev zlib1g-dev libncurses5-dev libmysqlclient-dev unzip
+        libpng-dev libssl-dev
+build:
+    urls:
+        - http://hgdownload.soe.ucsc.edu/admin/jksrc.v${version}.zip
+    commands:
+        - mkdir -p $HOME/bin/${arch}/ /build/dest/bin /build/dest/lib
+        - unzip jksrc.v${version}.zip
+        - cd kent/src/lib/
+        - make
+        - cd ../utils/
+        - COPT='-O -g -Wl,-rpath,$${ORIGIN}/../lib'
+        - ORIGIN='$ORIGIN'
+        - export COPT ORIGIN
+        - find . -type d -maxdepth 1 -mindepth 1 -exec make -C '{}' \;
+        - mv $HOME/bin/${arch}/* /build/dest/bin/
+        - |
+            for lib in $(ldd /build/dest/bin/faToTwoBit | grep -o '=> /[^ ]*' | sed 's/=> //g'); 
+            do
+                case $lib in
+                    */libcrypto.so*|*/libgcc_s.so*|*/libmysqlclient.so*|*/libssl.so*|*/libstdc++.so*)
+                        echo "including $lib";
+                        cp $lib /build/dest/lib/;
+                        ;;
+                esac
+            done
+        - tar zcf /host/${pkg}-${version}-Linux-${arch}.tar.gz -C /build/dest .
diff --git a/util/check-for-updates.py b/util/check-for-updates.py
new file mode 100644
index 00000000..f9fd80e8
--- /dev/null
+++ b/util/check-for-updates.py
@@ -0,0 +1,138 @@
+#!/usr/bin/env python
+import fnmatch
+import shutil
+import filecache
+import os
+import yaml
+import urllib2
+import json
+import re
+
+
+class UpdateFetcher(object):
+
+    def __init__(self):
+        self.packages = {}
+
+    def register_package(self, package, version):
+        if package not in self.packages:
+            self.packages[package] = []
+        self.packages[package].append(version)
+
+    def check_for_updates(self):
+        flu_kwattrs = {}
+        for package in self.packages:
+            if 'default' in self.packages[package]:
+                version = 'default'
+            else:
+                version = sorted(self.packages[package])[0]
+
+            if package in ('bcftools', 'samtools'):
+                flu_kwattrs['version_scheme'] = 'numbered'
+
+            urls = self.get_urls(package, version)
+            versioned_urls = [url for url in urls if '${' in url]
+            if len(versioned_urls) > 0:
+                for url in versioned_urls:
+                    latest_version = self.find_latest_url(url, **flu_kwattrs)
+
+                    # If that latest version doesn't have a folder all to itself...
+                    if latest_version is not None:
+                        if latest_version not in self.packages[package]:
+                            self.create_new_version(package, version, latest_version)
+                        else:
+                            print "Already have %s@%s" % (package, latest_version)
+
+    def create_new_version(self, package, version, latest):
+        """Given a package name, a version to copy from, and the version to
+        create...create a new folder for that version
+        """
+        print 'Creating %s %s %s' % (package, version, latest)
+
+        src_yml = os.path.join(package, version, 'build.yml')
+        dest = os.path.join(package, latest)
+        dest_yml = os.path.join(package, latest, 'build.yml')
+        os.mkdir(dest)
+
+        with open(dest_yml, 'w') as out_handle:
+            with open(src_yml, 'r') as in_handle:
+                data = yaml.load(in_handle)
+                data['meta']['version'] = latest
+                out_handle.write(yaml.dump(data, default_flow_style=False))
+
+    def get_urls(self, package, version):
+        with open(os.path.join(package, version, 'build.yml'), 'r') as handle:
+            data = yaml.load(handle)
+            return data.get('build', {}).get('urls', [])
+
+    @classmethod
+    def filter_version(cls, version_list, scheme):
+        if scheme == 'numbered':
+            return [v for v in version_list if re.match('^[0-9.]*$', v)]
+
+    @filecache.filecache(60 * 60 * 24)
+    def find_latest_url(self, url, version_scheme=None):
+        """Given a URL, find the most recent version of that available on the
+        website.
+
+        This is obviously not an error-free process, and will involve lots of
+        hardcoded data, however, if it replaces a human doing it, that's all we
+        need.
+        """
+
+        if 'github' in url:
+            url_parts = url.split('/')
+            username = url_parts[3]
+            reponame = url_parts[4]
+            if '/archive/' in url:
+                # Latest is tough here as we're downloading a specific revision
+                # number.
+                gh_api_url = 'https://api.github.com/repos/%s/%s/git/refs/heads/master' % (username, reponame)
+                gh_api_response = urllib2.urlopen(gh_api_url)
+                return json.load(gh_api_response).get('object', {}).get('sha', None)
+            elif 'releases/download' in url:
+                gh_api_url = 'https://api.github.com/repos/%s/%s/tags' % (username, reponame)
+                gh_api_response = urllib2.urlopen(gh_api_url)
+                try:
+                    versions = json.load(gh_api_response)
+                    good_versions = self.filter_version([x['name'] for x in versions], version_scheme)
+                    return good_versions[0]
+                    # Have to catch the case when it isn't a list
+                except Exception:
+                    return None
+            else:
+                print "Unknown github URL type %s" % url
+        elif 'hgdownload.soe.ucsc.edu' in url:
+            ucsc_url = 'http://hgdownload.soe.ucsc.edu/admin/'
+            ucsc_response = urllib2.urlopen(ucsc_url).read()
+            from bs4 import BeautifulSoup
+            soup = BeautifulSoup(ucsc_response)
+            versions = [x.text.replace('jksrc.v', '').replace('.zip', '')
+                        for x in soup.find_all('a') if 'jksrc.v' in x.text]
+            return str(sorted(map(int, versions))[-1])
+        elif 'emboss.open-bio' in url:
+            emboss_url = 'ftp://emboss.open-bio.org/pub/EMBOSS/'
+            emboss_response = urllib2.urlopen(emboss_url).read()
+            emboss_tar = [line for line in emboss_response.split('\n') if
+                          'EMBOSS-' in line and 'latest' not in line]
+            return emboss_tar[0].strip().split()[-1].replace('EMBOSS-', '').replace('.tar.gz', '')
+        else:
+            print "Updated unimplemented for %s" % url
+            return None
+        # http://downloads.sourceforge.net/project/math-atlas/Stable/${version}/atlas${version}.tar.bz2
+
+
+def main():
+    uf = UpdateFetcher()
+    for root, dirs, files in os.walk('.'):
+        for filename in files:
+            if fnmatch.fnmatch(filename, 'build.yml'):
+                package, version = os.path.split(root)
+                package = package[2:]
+                uf.register_package(package, version)
+
+    uf.check_for_updates()
+
+
+if __name__ == '__main__':
+    main()