diff --git a/.travis.yml b/.travis.yml
index c64b63699..1fb883b44 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,15 +1,14 @@
 language: python
+sudo: false
 
 matrix:
+    fast_finish: true
     include:
         - os: linux
-          sudo: false
           python: 2.7
         - os: linux
-          sudo: false
           python: 3.4
         - os: linux
-          sudo: false
           python: 3.5
 #        - os: osx
 #          language: generic
@@ -30,7 +29,12 @@ env:
   - PIP_DIR="$HOME/virtualenv"
   - GATK_PATH="$CACHE_DIR/GenomeAnalysisTK-3.6"
   - PYTHONIOENCODING=UTF8
+  # $BUNDLE_SECRET for decrypting tarball of third-party tools
   - secure: KX7DwKRD85S7NgspxevgbulTtV+jHQIiM6NBus2/Ur/P0RMdpt0EQQ2wDq79qGN70bvvkw901N7EjSYd+GWCAM7StXtaxnLRrrZ3XI1gX7KMk8E3QzPf0zualLDs7cuQmL6l6WiElUAEqumLc7WGpLZZLdSPzNqFSg+CBKCmTI8=
+  # $ANACONDA_TOKEN for uploading builds to anaconda.org ("broad-viral" channel) 
+  - secure: O+yKZxHthroiSi8KqMEF9qWDNv43iDXpk4rbhaZDlUKBiR5+AeXLR7OodWpX9LvhihpWgDoS5W42K0joPRP/rUJ2Jux9GH84Jhg+uDKN+XDi2sNT1/DsI4BTF0xxO0TeQ6IokbzV7idfW6gbhNoWMky7DnXtK6ruCJkkx4tWlno=
+  # $TRAVIS_ACCESS_TOKEN_FOR_OTHER_REPO (viral-ngs-deploy)
+  - secure: ChB0K3gPr5HknxYA41xCrpgChHDmLkqc79p1NABB/tbqOEnrPzDPqE+FU4/QlmeV96jMYn4uyLVauJpzVXyBIVoOa8guqoF5VdiKlAhaUwh9UQJ75i3SKQtGBrqaTXSDVI1vJARMiGabduCrcNJxVsxV9Bm+YzTq6tuhWyqR4fs=
 
 git:
   depth: 3
@@ -49,3 +53,10 @@ script:
 
 after_success:
   - coveralls
+
+deploy:
+  provider: script
+  script: travis/deploy.sh $TRAVIS_TAG
+  on:
+    tags: true
+    #all_branches: true
diff --git a/packaging/conda-recipe/render-recipe.py b/packaging/conda-recipe/render-recipe.py
new file mode 100755
index 000000000..f801c279a
--- /dev/null
+++ b/packaging/conda-recipe/render-recipe.py
@@ -0,0 +1,289 @@
+#!/usr/bin/python
+
+# stdlib
+import os, sys, re
+import glob
+import jinja2
+import json
+import pprint
+import argparse
+import hashlib
+import time
+# since py3 split up urllib
+try:
+    from urllib.request import urlopen
+except ImportError:
+    from urllib2 import urlopen
+
+"""
+Renders Jinja2 templates using variables from dependency files
+
+The behavior is not (yet) recursive.
+"""
+
+input_directory = "viral-ngs-template"
+output_directory = "viral-ngs"
+source_url = ""
+
+dir_path = os.path.dirname(os.path.realpath(__file__))
+
+class VersionString(object):
+    """
+        Class to validate and parse PEP440 version strings (also used by conda)
+        Shortened and derived from: https://github.com/pypa/packaging/blob/16.7/packaging/version.py
+    """
+
+    VERSION_PATTERN = r"""
+    (?P<prefix>v?)
+    (?:
+        (?:(?P<epoch>[0-9]+)!)?                           # epoch
+        (?P<release>[0-9]+(?:\.[0-9]+)*)                  # release segment
+        (?P<pre>                                          # pre-release
+            [-_\.]?
+            (?P<pre_l>(a|b|c|rc|alpha|beta|pre|preview))
+            [-_\.]?
+            (?P<pre_n>[0-9]+)?
+        )?
+        (?P<post>                                         # post release
+            (?:-(?P<post_n1>[0-9]+))
+            |
+            (?:
+                [-_\.]?
+                (?P<post_l>post|rev|r)
+                [-_\.]?
+                (?P<post_n2>[0-9]+)?
+            )
+        )?
+        (?P<dev>                                          # dev release
+            [-_\.]?
+            (?P<dev_l>dev)
+            [-_\.]?
+            (?P<dev_n>[0-9]+)?
+        )?
+    )
+    (?:\+(?P<local>[a-z0-9]+(?:[-_\.][a-z0-9]+)*))?       # local version
+    """
+    version_re = re.compile(
+        r"^\s*" + VERSION_PATTERN + r"\s*$",
+        re.VERBOSE | re.IGNORECASE,)
+
+    def __init__(self, v):
+        self.v = v
+
+    def __str__(self):
+        parts = []
+
+        try:
+            # 'v' prefix
+            if self.version_re.match(self.v).group("prefix") is not None:
+                parts.append("{0}".format(self.version_re.match(self.v).group("prefix")))
+
+            # Epoch
+            if ( int(self.version_re.match(self.v).group("epoch")) if self.version_re.match(self.v).group("epoch") else 0) != 0:
+                parts.append("{0}!".format(self.version_re.match(self.v).group("epoch")))
+
+            # Release segment
+            parts.append(".".join(str(x) for x in self.version_re.match(self.v).group("release").split(".")))
+
+            # Pre-release
+            if self.version_re.match(self.v).group("pre") is not None:
+                parts.append("".join(str(x) for x in self.version_re.match(self.v).group("pre")))
+
+            # Post-release
+            if self.version_re.match(self.v).group("post") is not None:
+                parts.append(".post{0}".format(self.version_re.match(self.v).group("post")))
+
+            # Development release
+            if self.version_re.match(self.v).group("dev") is not None:
+                parts.append(".dev{0}".format(self.version_re.match(self.v).group("dev")))
+
+            # Local version segment
+            if self.version_re.match(self.v).group("local") is not None:
+                parts.append(
+                    "+{0}".format(".".join(str(x) for x in self.version_re.match(self.v).group("local")))
+                )
+        except:
+            raise argparse.ArgumentTypeError("String '%s' does not match required PEP440 format"%(self.v,))
+
+        return "".join(parts)
+
+
+def reformat_package_line(line):
+    """
+    This function is meant to take a package spec in conda or pip format
+    and return one in conda recipe format: https://conda.io/docs/spec.html
+    """
+    # regex to match comment-only line
+    comment_re = re.compile(r"^(?:\s*\#.*)$")
+
+    # regex to match package spec line, with support for comments and selectors.
+    # This will also capture hash-indicated selectors and comments (ex. "# [osx]")
+    # which may, or may not, be useful in their original context.
+    package_re = re.compile(r"^(?P<package>[a-zA-Z0-9\-\_]+)(?:\s*)(?:(?P<comparator>[\>\<=]?=?)(?:\s*)(?P<version>[^\s\#=]+)(?:=(?P<build>[0-9]*))?(?:\s*))?(?P<selector>\s*\#\s*\[.*\])?(?P<comment>\s*\#.*)?$")
+
+    # when we need to specify a different comparator for the recipe
+    comparator_replacements = {
+        "=": "==",
+    }
+
+    # the line shold not have a newline
+    line = line.replace("\n","").replace("\r","")
+
+    # if the line is a comment, simpy return it
+    if len(line)==0 or comment_re.match(line):
+        return line
+    # otherwise, build a package spec string suitable for a conda recipe
+    else: 
+        m = package_re.match(line)
+        recipe_package_string = "- {package} {comparator}{version}{build}{selector}{comment}".format(
+            package    = m.group("package").lower(), # conda packages must have lowercase names
+            comparator = "" if not m.group("comparator") else comparator_replacements.get(m.group("comparator"), m.group("comparator")),
+            version    = "" if not m.group("version") else m.group("version"),
+            build      = "" if not m.group("build") else " "+m.group("build")+"*", # Todo: verify build separator character for recip format
+            selector   = "" if not m.group("selector") else " "+m.group("selector"),
+            comment    = "" if not m.group("comment") else " "+m.group("comment")
+        )
+        return recipe_package_string
+
+def url_md5(url):
+    hash_md5 = hashlib.md5()
+    CHUNK_SIZE = 16 * 1024
+
+    # try four times to download the file. If one fails, wait two seconds and try again.
+    try_count = 1
+    while True:
+        try:
+            print("Downloading source package for hash calculation...")
+            response = urlopen(url)
+            for chunk in iter(lambda: response.read(CHUNK_SIZE), b""):
+                hash_md5.update(chunk)
+            break
+        except:
+            print("Download {} failed, sleeping then retrying...".format(try_count))
+            try_count +=1
+            if try_count >3:
+                raise
+            time.sleep(2)
+            continue
+
+    return hash_md5.hexdigest()
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser(description='Renger the conda recipe.')
+    parser.add_argument('version',
+                        type=VersionString,
+                        help='the version number of the package')
+    parser.add_argument('--build-reqs', nargs='*', dest='build_requirements',
+                        type=argparse.FileType('r'),
+                        help='build-time requirements file')
+    parser.add_argument('--run-reqs', nargs='*', dest='run_requirements',
+                        type=argparse.FileType('r'),
+                        help='run-time requirements file')
+    parser.add_argument('--py2-run-reqs', nargs='*', dest='py2_run_requirements',
+                        type=argparse.FileType('r'),
+                        help='python2-only run-time requirements file')
+    parser.add_argument('--py3-run-reqs', nargs='*', dest='py3_run_requirements',
+                        type=argparse.FileType('r'),
+                        help='python3-only run-time requirements file')
+    parser.add_argument('--linux-run-reqs', nargs='*', dest='linux_run_requirements',
+                        type=argparse.FileType('r'),
+                        help='linux-only run-time requirements file')
+    parser.add_argument('--osx-run-reqs', nargs='*', dest='osx_run_requirements',
+                        type=argparse.FileType('r'),
+                        help='osx-only run-time requirements file')
+    parser.add_argument('--test-reqs', nargs='*', dest='test_requirements',
+                        type=argparse.FileType('r'),
+                        help='test-time requirements file')
+
+    try:
+       args = parser.parse_args()
+       if not any(vars(args).values()):
+            parser.print_help()
+            sys.exit(0)
+    except:
+        sys.exit(0)
+
+    args_dict = vars(args)
+
+    recipe_variables = {}
+
+    # store two separate version strings, one to use for the conda package and one
+    # that should match github tagged releases
+    recipe_variables["PKG_VERSION"] = str(args_dict.pop("version"))
+
+    # strip "v" prefix from versions that look like v1.14.0
+    if recipe_variables["PKG_VERSION"].startswith("v"):
+        recipe_variables["PKG_VERSION_CONDA"] = recipe_variables["PKG_VERSION"][1:]
+    else:
+        recipe_variables["PKG_VERSION_CONDA"] = recipe_variables["PKG_VERSION"]
+
+    # after we pop the positional argument(s), the optional ones remaining are all files
+    for var_name, req_files in args_dict.items():
+        if req_files:
+            for reqs_file in req_files:
+                if reqs_file:
+                    recipe_variables[var_name] = []
+                    for line in reqs_file:
+                        conda_style_package_line = reformat_package_line(line)
+                        if len(conda_style_package_line):
+                            recipe_variables[var_name].append(conda_style_package_line)
+    pprint.pprint(recipe_variables)
+
+    j_env = jinja2.Environment(loader=jinja2.FileSystemLoader(os.path.join(dir_path, input_directory)))
+
+    if not os.path.exists(output_directory):
+        os.makedirs(output_directory)
+
+    template_files = os.listdir(os.path.join(dir_path,input_directory))
+
+    for template_file in template_files:
+        print("Rendering "+ template_file)
+        # jinja expects the filename to be just that, not a path
+        # it should be relative to the FileSystemLoader() path set above
+        template = j_env.get_template(template_file)
+        output_from_parsed_template = template.render(recipe_variables)
+
+        # save the rendered output
+        with open(os.path.join(dir_path, output_directory, template_file), "wb") as f:
+            f.write(output_from_parsed_template)
+
+        # populate md5 hashes for any source urls present
+        if(template_file.endswith(".yaml")):
+            # calculate and add md5 hashes to recipe
+            with open(os.path.join(dir_path, output_directory, template_file), "rb") as inf:
+                with open(os.path.join(dir_path, output_directory, template_file+".checksumed"), "wb") as outf:
+                    for line in inf:
+                        # if this is an md5 line, don't write it out
+                        if line.strip().startswith("md5"):
+                            continue
+                        # if this is not an md5 line, write it verbatim
+                        else:
+                            outf.writelines([line])
+
+                            # if this is a url line
+                            if line.strip().startswith("url"):
+                                # parse out the url
+                                url_re = re.compile(r"^(?:(?P<leadingspace>\s*)url:\s*)(?P<url>[\S]*)(?P<extra>.*)$")
+                                matches = url_re.match(line)
+                                if matches:
+                                    if matches.group("url"):
+                                        # download file and calculate md5
+                                        src_hash = url_md5(matches.group("url"))
+                                        hash_line = "{leadingspace}md5: {src_hash}{extra}".format(
+                                            leadingspace="" if not matches.group("leadingspace") else matches.group("leadingspace"),
+                                            src_hash=src_hash,
+                                            extra="" if not matches.group("extra") else matches.group("extra")
+                                        )
+                                        outf.writelines([hash_line+"\n"])
+
+                                    else:
+                                        raise Exception("The yaml file url line does not appear to contain a url")
+
+
+            # move the file with checksums
+            os.rename(os.path.join(dir_path, output_directory, template_file+".checksumed"), os.path.join(dir_path, output_directory, template_file))
+
+
+
+
diff --git a/packaging/conda-recipe/viral-ngs-template/build.sh b/packaging/conda-recipe/viral-ngs-template/build.sh
new file mode 100644
index 000000000..22991b872
--- /dev/null
+++ b/packaging/conda-recipe/viral-ngs-template/build.sh
@@ -0,0 +1,22 @@
+#!/bin/bash
+
+BINARY_HOME=$PREFIX/bin
+PACKAGE_HOME=$PREFIX/opt/$PKG_NAME-$PKG_VERSION
+
+cd $SRC_DIR
+
+# remove files duplicated by conda packages
+rm tools/binaries/V-Phaser-2.0/MacOSX/libgomp.1.dylib
+#chmod +x tools/scripts/*
+
+find tools/scripts/ -name "*.py" -exec chmod +x {} \;
+find tools/scripts/ -name "*.sh" -exec chmod +x {} \;
+
+# copy source to bin
+mkdir -p $PREFIX/bin
+mkdir -p $PACKAGE_HOME
+cp -R $SRC_DIR/* $PACKAGE_HOME/
+cd $PACKAGE_HOME && chmod a+x *.py
+
+cd $PACKAGE_HOME
+find *.py -type f -exec ln -s $PACKAGE_HOME/{} $BINARY_HOME/{} \;
diff --git a/packaging/conda-recipe/viral-ngs-template/meta.yaml b/packaging/conda-recipe/viral-ngs-template/meta.yaml
new file mode 100644
index 000000000..640bfd012
--- /dev/null
+++ b/packaging/conda-recipe/viral-ngs-template/meta.yaml
@@ -0,0 +1,93 @@
+package:
+  name: viral-ngs
+  version: {{PKG_VERSION_CONDA}}
+
+about:
+  home: https://github.com/broadinstitute/viral-ngs
+  license: https://raw.githubusercontent.com/broadinstitute/viral-ngs/master/LICENSE
+  summary: A set of scripts and tools for the analysis of viral NGS data
+
+source:
+  fn: viral-ngs-{{PKG_VERSION}}.zip
+  url: https://github.com/broadinstitute/viral-ngs/archive/{{PKG_VERSION}}.zip
+
+build:
+    number: 0
+    rpaths:
+        - lib/
+        - lib//
+
+requirements:
+  build:
+    - python
+    - java-jdk >=7
+    - perl
+    {% for item in build_requirements %}
+    {{ item }}
+    {%- endfor %}
+    # C lib or compilation-related
+    - gcc   # [not osx]
+    - llvm  # [osx]
+    - boost 1.61* # needed for diamond, among other packages
+
+  run:
+    - python
+    - java-jdk >=7
+    - perl
+    {% for item in run_requirements %}
+    {{ item }}
+    {%- endfor %}
+    {% for item in py2_run_requirements %}
+    {{ item }} # [py2k]
+    {%- endfor %}
+    {% for item in py3_run_requirements %}
+    {{ item }} # [py3k]
+    {%- endfor %}
+    {% for item in linux_run_requirements %}
+    {{ item }} # [linux]
+    {%- endfor %}
+    {% for item in osx_run_requirements %}
+    {{ item }} # [osx]
+    {%- endfor %}
+    # C lib-related
+    - libgcc # [not osx]
+    - boost 1.61* # needed for diamond, among other packages
+
+test:
+  requires:
+    # testing-related
+    {% for item in test_requirements %}
+    {{ item }}
+    {%- endfor %}
+  commands:
+    # test command-line tools
+    - "assembly.py -h &> /dev/null"
+    - "broad_utils.py -h &> /dev/null"
+    - "illumina.py -h &> /dev/null"
+    - "interhost.py -h &> /dev/null"
+    - "intrahost.py -h &> /dev/null"
+    - "metagenomics.py -h &> /dev/null"
+    - "ncbi.py -h &> /dev/null"
+    - "read_utils.py -h &> /dev/null"
+    - "reports.py -h &> /dev/null"
+    - "taxon_filter.py -h &> /dev/null"
+
+    # test tool install
+    #- "cd $PREFIX/opt/$PKG_NAME-$PKG_VERSION && py.test -v test/unit/test_tools.py"
+
+    # various unit tests
+    #cd 
+    - "cd $PREFIX/opt/$PKG_NAME-$PKG_VERSION && py.test -v test/unit/test_tools_vphaser2.py"
+    - "cd $PREFIX/opt/$PKG_NAME-$PKG_VERSION && py.test -v test/unit/test_tools_picard.py"
+    - "cd $PREFIX/opt/$PKG_NAME-$PKG_VERSION && py.test -v test/unit/test_tools_samtools.py"
+    - "cd $PREFIX/opt/$PKG_NAME-$PKG_VERSION && py.test -v test/unit/test_taxon_filter.py"
+    - "cd $PREFIX/opt/$PKG_NAME-$PKG_VERSION && py.test -v test/unit/test_util_misc.py"
+    - "cd $PREFIX/opt/$PKG_NAME-$PKG_VERSION && py.test -v test/unit/test_util_vcf.py"    
+    - "cd $PREFIX/opt/$PKG_NAME-$PKG_VERSION && py.test -v test/unit/test_snake.py" # [py3k]
+    #- "cd $PREFIX/opt/$PKG_NAME-$PKG_VERSION && py.test -v test/unit/test_read_utils.py"
+    #- "cd $(dirname $(which illumina.py))/../opt/$PKG_NAME-$PKG_VERSION && py.test -v test/unit/test_tools_novoalign.py"
+
+    #- "cd $PREFIX/opt/$PKG_NAME-$PKG_VERSION && py.test -v test/unit/test_interhost.py"
+    #- "cd $PREFIX/opt/$PKG_NAME-$PKG_VERSION && py.test -v test/unit/test_intrahost.py"
+    #- "cd $PREFIX/opt/$PKG_NAME-$PKG_VERSION && py.test -v test/unit/test_assembly.py"
+    #- "cd $PREFIX/opt/$PKG_NAME-$PKG_VERSION && py.test -v test/unit/test_illumina.py"
diff --git a/packaging/conda-recipe/viral-ngs-template/post-link.sh b/packaging/conda-recipe/viral-ngs-template/post-link.sh
new file mode 100644
index 000000000..3c9bbf0d5
--- /dev/null
+++ b/packaging/conda-recipe/viral-ngs-template/post-link.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+echo "viral-ngs depends on GATK"
+# call gatk-register which will print its usage statement
+$PREFIX/bin/gatk-register
+
+# exit 0 so the install is a success
+exit 0 
diff --git a/packaging/conda-recipe/viral-ngs/.gitignore b/packaging/conda-recipe/viral-ngs/.gitignore
new file mode 100644
index 000000000..db1714674
--- /dev/null
+++ b/packaging/conda-recipe/viral-ngs/.gitignore
@@ -0,0 +1,6 @@
+# this directory is a placeholder to contain jinja2-rendered
+# conda recipes, so the files in it should be ignored
+
+*
+*/
+!.gitignore
\ No newline at end of file
diff --git a/requirements-conda.txt b/requirements-conda.txt
index d63683dca..146c79067 100644
--- a/requirements-conda.txt
+++ b/requirements-conda.txt
@@ -3,13 +3,13 @@ bmtagger=3.101
 bwa=0.7.15
 diamond=0.8.22=2
 gatk=3.6
-kraken-all=0.10.6_eaf8fb68
+kraken-all=0.10.6_eaf8fb68 # [linux]
 krona=2.7
 last=719
 fastqc=0.11.5
 mafft=7.221
-mummer=3.23
-muscle=3.8.1551
+mummer=3.23 
+muscle=3.8.1551 
 mvicuna=1.0
 novoalign=3.06.05
 picard=2.5.0
@@ -23,13 +23,16 @@ vphaser2=2.0
 biopython=1.68
 matplotlib=1.5.3
 future>=0.15.2
-PyYAML=3.11
 pysam=0.9.1
+bedtools=2.26.0
+pybedtools=0.7.8
+PyYAML==3.11
+pytest==3.0.5
 pycodestyle
 mock==2.0.0
 six<2
-pytest=3.0.5
-pytest-cov=2.4.0
-pytest-xdist=1.15.0
-bedtools=2.26.0
-pybedtools=0.7.8
+pytest-cov==2.4.0
+pytest-catchlog==1.2.2
+pytest-xdist==1.15.0
+flake8<=3
+Jinja2==2.8
\ No newline at end of file
diff --git a/requirements-docs.txt b/requirements-docs.txt
deleted file mode 100644
index b88d7b246..000000000
--- a/requirements-docs.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-Sphinx==1.4.4
-sphinx-argparse==0.1.14
-boltons==15.0.0
-sphinx-rtd-theme==0.1.9
-matplotlib==1.5.3
diff --git a/requirements-pipes.txt b/requirements-pipes.txt
deleted file mode 100644
index fd45218aa..000000000
--- a/requirements-pipes.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-boto==2.38.0
-snakemake==3.9.0
-PyYAML==3.11
diff --git a/requirements-py-docs.txt b/requirements-py-docs.txt
new file mode 100644
index 000000000..cb711cce1
--- /dev/null
+++ b/requirements-py-docs.txt
@@ -0,0 +1,4 @@
+Sphinx==1.4.4
+sphinx-argparse==0.1.15
+sphinx_rtd_theme==0.1.9
+matplotlib==1.5.3
diff --git a/requirements-py-tests.txt b/requirements-py-tests.txt
new file mode 100644
index 000000000..530edf62a
--- /dev/null
+++ b/requirements-py-tests.txt
@@ -0,0 +1 @@
+coveralls==1.1
\ No newline at end of file
diff --git a/requirements-py2.txt b/requirements-py2.txt
new file mode 100644
index 000000000..4b9d1a68e
--- /dev/null
+++ b/requirements-py2.txt
@@ -0,0 +1 @@
+futures==3.0.3
\ No newline at end of file
diff --git a/requirements-py3.txt b/requirements-py3.txt
new file mode 100644
index 000000000..7df4593fa
--- /dev/null
+++ b/requirements-py3.txt
@@ -0,0 +1,2 @@
+boto==2.38.0
+snakemake==3.9.0
\ No newline at end of file
diff --git a/requirements-tests.txt b/requirements-tests.txt
deleted file mode 100644
index dd0153b0d..000000000
--- a/requirements-tests.txt
+++ /dev/null
@@ -1,8 +0,0 @@
-pytest==3.0.5
-coveralls==1.1
-pycodestyle
-mock==2.0.0
-six<2
-pytest-cov==2.4.0
-pytest-logging==2015.11.4
-pytest-xdist==1.15.0
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 920749abb..000000000
--- a/requirements.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-# Package source, listed here for clarity:
---index-url https://pypi.python.org/simple/
-
-futures==3.0.3; python_version == '2.6' or python_version=='2.7'
diff --git a/travis/deploy.sh b/travis/deploy.sh
new file mode 100755
index 000000000..3462974b8
--- /dev/null
+++ b/travis/deploy.sh
@@ -0,0 +1,49 @@
+#!/bin/bash
+
+# This script performs various packing and deployment operations.
+# It assumes it will be caused as a deploy hook of TravisCI; ex.:
+#
+# deploy:
+#   provider: script
+#   script: travis/deploy.sh $TRAVIS_TAG
+#   on:
+#     tags: true
+#     all_branches: master
+
+
+# way to get the absolute path to this script that should
+# work regardless of whether or not this script has been sourced
+# Find original directory of bash script, resovling symlinks
+# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128
+SOURCE="${BASH_SOURCE[0]}"
+while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+    DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+    if [[ "$OSTYPE" == "darwin"* ]]; then
+        SOURCE="$(readlink "$SOURCE")"
+    else
+        SOURCE="$(readlink -f "$SOURCE")"
+    fi
+    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+done
+SCRIPT=$SOURCE
+SCRIPT_DIRNAME="$(dirname "$SOURCE")"
+SCRIPTPATH="$(cd -P "$(echo $SCRIPT_DIRNAME)" &> /dev/null && pwd)"
+SCRIPT="$SCRIPTPATH/$(basename "$SCRIPT")"
+
+PKG_VERSION=$1
+
+# === Build conda package and upload
+
+# if the ANACONDA_TOKEN is defined (not on an external branch)
+if [ ! -z "$ANACONDA_TOKEN" ]; then
+    echo "Running $SCRIPTPATH/package-conda.sh"
+    # Render recipe from template and dependency files, setting the tag as the current version
+    packaging/conda-recipe/render-recipe.py $PKG_VERSION --build-reqs requirements-conda.txt --run-reqs requirements-conda.txt --py3-run-reqs requirements-py3.txt --py2-run-reqs requirements-py2.txt
+    if conda build --python $TRAVIS_PYTHON_VERSION --token $ANACONDA_TOKEN packaging/conda-recipe/viral-ngs; then
+        # check the exit code of conda build, and if successful,
+        # trigger the viral-ngs-deploy repository to test/build the docker container
+        ./travis/trigger-tests-in-other-repo.sh
+    fi
+else
+    echo "ANACONDA_TOKEN is not defined. Conda package upload is only supported for branches on the original repository."
+fi
diff --git a/travis/install-conda.sh b/travis/install-conda.sh
index 57fd63bbe..786ef7ca7 100755
--- a/travis/install-conda.sh
+++ b/travis/install-conda.sh
@@ -40,11 +40,13 @@ else # if it does not exist, we need to install miniconda
     fi
     hash -r
     conda config --set always_yes yes --set changeps1 no
+    conda config --set anaconda_upload yes # for uploading packages after successful build
     conda config --add channels bioconda
     conda config --add channels r
     conda config --add channels conda-forge
-    conda update -y -q conda
-    conda install java-jdk==8.0.92
+    conda install -y -q conda=4.2 # pin to 4.2.* until this is fixed: https://github.com/conda/conda-build/issues/1666
+    conda config --set auto_update_conda false
+    conda install -y java-jdk==8.0.92
 fi
 
 conda info -a # for debugging
diff --git a/travis/install-pip.sh b/travis/install-pip.sh
index 082f6da7c..2885ddad6 100755
--- a/travis/install-pip.sh
+++ b/travis/install-pip.sh
@@ -2,16 +2,19 @@
 set -e
 
 echo "pip installing required python packages"
-pip install -r requirements.txt
+#pip install -r requirements.txt
 
 #PYVER=`python -V 2>&1 | cut -c 8`
 PYVER=`echo $TRAVIS_PYTHON_VERSION | cut -c 1`
 if [ "$PYVER" = "3" ]; then
     echo "pip installing snakemake packages (py3 only)"
-    pip install -r requirements-pipes.txt
+    pip install -r requirements-py3.txt
+elif [ "$PYVER" = "2" ]; then
+    echo "pip install py2 packages"
+    pip install -r requirements-py2.txt
 fi
 
 python --version
 
 echo "pip installing test-related packages (coveralls, etc.)"
-pip install -r requirements-tests.txt
+pip install -r requirements-py-tests.txt
diff --git a/travis/tests-long.sh b/travis/tests-long.sh
index 355a593fb..6b1bc6d71 100755
--- a/travis/tests-long.sh
+++ b/travis/tests-long.sh
@@ -3,6 +3,7 @@ set -e
 
 echo "TRAVIS_BRANCH: $TRAVIS_BRANCH"
 echo "TRAVIS_PULL_REQUEST: $TRAVIS_PULL_REQUEST"
+echo "TRAVIS_TAG: $TRAVIS_TAG"
 
 if [ $TRAVIS_PULL_REQUEST != "false" -o $TRAVIS_BRANCH = "master" -o -n "$TRAVIS_TAG" ]; then
     echo "This is on master or is a pull request: executing long running tests..."
diff --git a/travis/trigger-tests-in-other-repo.sh b/travis/trigger-tests-in-other-repo.sh
new file mode 100644
index 000000000..cbe511298
--- /dev/null
+++ b/travis/trigger-tests-in-other-repo.sh
@@ -0,0 +1,16 @@
+#!/bin/bash
+
+echo "Script called to trigger tests in external repository..."
+
+# only initiate tests in other repo if the travis token string has a value
+if [ ! -z "$TRAVIS_ACCESS_TOKEN_FOR_OTHER_REPO" ]; then
+    echo "TRAVIS_ACCESS_TOKEN_FOR_OTHER_REPO is defined"
+        # if this is a tagged release add that information to the dependent build request
+    if [ -n "$TRAVIS_TAG" ]; then
+        ./travis/trigger-travis.sh --script "env UPSTREAM_BRANCH=$TRAVIS_BRANCH UPSTREAM_TAG=$TRAVIS_TAG bash ./travis/tests-long.sh" broadinstitute viral-ngs-deploy $TRAVIS_ACCESS_TOKEN_FOR_OTHER_REPO "UPSTREAM_BRANCH=$TRAVIS_BRANCH UPSTREAM_TAG=$TRAVIS_TAG"
+    else
+        ./travis/trigger-travis.sh --script "env UPSTREAM_BRANCH=$TRAVIS_BRANCH ./travis/tests-long.sh" broadinstitute viral-ngs-deploy $TRAVIS_ACCESS_TOKEN_FOR_OTHER_REPO "UPSTREAM_BRANCH=$TRAVIS_BRANCH"
+    fi
+else
+    echo "TRAVIS_ACCESS_TOKEN_FOR_OTHER_REPO is undefined. Check the secure variable."
+fi
\ No newline at end of file
diff --git a/travis/trigger-travis.sh b/travis/trigger-travis.sh
new file mode 100644
index 000000000..a33802856
--- /dev/null
+++ b/travis/trigger-travis.sh
@@ -0,0 +1,181 @@
+#!/bin/sh -f
+
+# Derived from: https://github.com/mernst/plume-lib/blob/master/bin/trigger-travis.sh
+# Which is originally under an MIT license
+
+# Trigger a new Travis-CI job.
+# Ordinarily, a new Travis job is triggered when a commit is pushed to a
+# GitHub repository.  The trigger-travis.sh script provides a programmatic
+# way to trigger a new Travis job.
+
+# Usage:
+#   trigger-travis.sh [--pro] [--branch BRANCH] GITHUBID GITHUBPROJECT TRAVIS_ACCESS_TOKEN [MESSAGE]
+# For example:
+#   trigger-travis.sh typetools checker-framework `cat ~/private/.travis-access-token` "Trigger for testing"
+#
+# where --pro means to use travis-ci.com instead of travis-ci.org, and
+# where TRAVIS_ACCESS_TOKEN is, or ~/private/.travis-access-token contains,
+# the Travis access token.
+#
+# Your Travis access token is the text after "Your access token is " in
+# the ouput of these commands:
+#   travis login && travis token
+# (If the travis program isn't installed, do so with one of these two commands:
+#    gem install travis
+#    sudo apt-get install ruby-dev && sudo gem install travis
+# Don't do "sudo apt-get install travis" which installs a trajectory analyzer.)
+# Note that the Travis access token output by `travis token` differs from the
+# Travis token available at https://travis-ci.org/profile .
+# If you store it in in a file, make sure the file is not readable by others,
+# for example by running:  chmod og-rwx ~/private
+
+# To use this script to trigger a dependent build in Travis, do two things:
+#
+# 1. Set an environment variable TRAVIS_ACCESS_TOKEN by navigating to
+#   https://travis-ci.org/MYGITHUBID/MYGITHUBPROJECT/settings
+# The TRAVIS_ACCESS_TOKEN environment variable will be set when Travis runs
+# the job, but won't be visible to anyone browsing https://travis-ci.org/.
+#
+# 2. Add the following before_install and after_script block to your
+# .travis.yml file, where you replace OTHERGITHUB* by a specific downstream
+# project, but you leave $TRAVIS_ACCESS_TOKEN as literal text:
+#
+# before_install:
+#   - npm install --save-dev travis-after-all
+#
+# after_script:
+#   - |
+#       declare exitCode;
+#       $(npm bin)/travis-after-all
+#       exitCode=$?
+#
+#       if [ "$exitCode" -eq 0 ]; then
+#         if [[ ($TRAVIS_BRANCH == master) &&
+#               ($TRAVIS_PULL_REQUEST == false) ]] ; then
+#           curl -LO https://raw.github.com/mernst/plume-lib/master/bin/trigger-travis.sh
+#           sh trigger-travis.sh OTHERGITHUBID OTHERGITHUBPROJECT $TRAVIS_ACCESS_TOKEN
+#         fi
+#       fi
+#
+# Your .travis.yml file must not use `language: generic` because then
+# npm won't be installed.
+#
+# Note that Travis does not fail a job if an after_success command fails.
+# If you misspell a GitHub ID or project name, then this script will fail,
+# but Travis won't inform you of the mistake.  So, check the end of the
+# Travis build log the first time that a build succeeds.
+
+# Here is an explanation of the conditional in the after_success block:
+#
+# 1. Downstream projects are triggered only for builds of the mainline, not
+# branches or pull requests.  The reason is that typically a downstream
+# project clones and uses the mainline.  You could enhance this script to
+# accept pass an environment variable for the upstream project; the
+# downstream project's build script would need to read and use that
+# environment variable.  If you make this enhancement, feel free to submit
+# a pull request so that others can benefit from it.
+#
+# 2. Downstream projects are triggered only if the Travis job number
+# contains no "." or ends with ".1".  In other words, if your .travis.yml
+# defines a build matrix
+# (https://docs.travis-ci.com/user/customizing-the-build/#Build-Matrix)
+# that runs the same job using different configurations, then the
+# "after_success:" block is run only for the first configuration.
+# By default an after_success: block is run for every build in the matrix,
+# but you really want it to run once if all the builds in the matrix
+# succeed.  Running if the first job succeeds is simple and it is usually
+# adequate, even though the downstream job is triggered even if some job
+# other than the first one fails.
+
+# TODO: enable the script to clone a particular branch rather than master.
+# This would require a way to know the relationships among branches in
+# different GitHub projects.  It's easier to run all your tests within a
+# single Travis job, if they fit within Travis's 50-minute time limit.
+
+# An alternative to this script would be to install the Travis command-line
+# client and then run:
+#   travis restart -r OTHERGITHUBID/OTHERGITHUBPROJECT
+# That is undesirable because it restarts an old job, destroying its history,
+# rather than starting a new job which is our goal.
+
+# Parts of this script were originally taken from
+# http://docs.travis-ci.com/user/triggering-builds/
+
+# TODO: take a --branch command-line argument.
+
+if [ "$#" -lt 3 ] || [ "$#" -ge 7 ]; then
+  echo "Wrong number of arguments $# to trigger-travis.sh; run like:"
+  echo " trigger-travis.sh [--pro] [--script 'script value...'] [--branch BRANCH] GITHUBID GITHUBPROJECT TRAVIS_ACCESS_TOKEN [MESSAGE]" >&2
+  exit 1
+fi
+
+if [ "$1" = "--pro" ] ; then
+  TRAVIS_URL=travis-ci.com
+  shift
+else
+  TRAVIS_URL=travis-ci.org
+fi
+
+if [ "$1" = "--branch" ] ; then
+  shift
+  BRANCH="$1"
+  shift
+else
+  BRANCH=master
+fi
+
+if [ "$1" = "--script" ] ; then
+  shift
+  SCRIPT_VAL="$1"
+  shift
+else
+  SCRIPT_VAL=""
+fi
+
+USER=$1
+REPO=$2
+TOKEN=$3
+if [ $# -eq 4 ] ; then
+    MESSAGE=",\"message\": \"$4\""
+elif [ -n "$TRAVIS_REPO_SLUG" ] ; then
+    MESSAGE=",\"message\": \"Triggered by upstream build of $TRAVIS_REPO_SLUG commit "`git rev-parse --short HEAD`"\""
+else
+    MESSAGE=""
+fi
+
+if [ -n "$SCRIPT_VAL" ]; then
+  SCRIPT_BODY="\"script\": \"$SCRIPT_VAL\""
+else
+  SCRIPT_BODY=""
+fi
+
+body="{
+\"request\": {
+  \"branch\":\"$BRANCH\"$MESSAGE,
+
+  \"config\":{
+  $SCRIPT_BODY
+}}}"
+
+echo "Travis API request body:\n$body"
+
+#exit 0
+
+echo "Making request to start tests in other repository..."
+
+# It does not work to put / in place of %2F in the URL below. 
+curl -s -X POST \
+  -H "Content-Type: application/json" \
+  -H "Accept: application/json" \
+  -H "Travis-API-Version: 3" \
+  -H "Authorization: token ${TOKEN}" \
+  -d "$body" \
+  https://api.${TRAVIS_URL}/repo/${USER}%2F${REPO}/requests \
+ | tee /tmp/travis-request-output.$$.txt
+
+if grep -q '"@type": "error"' /tmp/travis-request-output.$$.txt; then
+    exit 1
+fi
+if grep -q 'access denied' /tmp/travis-request-output.$$.txt; then
+    exit 1
+fi
\ No newline at end of file