travis-ci.ORG -> travis-ci.COM (#910)

* travis-ci.ORG -> travis-ci.COM

Update the badge to reflect a transition from the .org version of TravisCI to the .com version, in support of a migration from the deprecated GitHub service integration to the new "app."

* travis-ci.org -> travis-ci.com

* update some of the encrypted secrets

* encrypt secrets for travis-ci.COM

encrypt secrets for travis-ci.COM  via "travis encrypt --com"

* revise DNAnexus Travis token

* update Quay.io credentials for Travis-ci.com

.travis.yml

@@ -47,15 +47,15 @@ jobs:
       env:
         - TRAVIS_JOB=docker_wdl
         # DOCKER_USER (for Quay.io)
-        - secure: R5NXHDxFzoogYf2qlk9O0G7xWJ8JCD/y4XA06Vq902udfFWy+O4h7ftGTHjwQdyufrZFUZEhXNbXPX/xMTn73u/puKr5m4lm8Bg1aVDUumyDmyQqxwQsnSF0fOld+FEG5j1FnT7Mf5V+F96KUH6/YXjndAjYxGSEUsJQ+C413YY=
+        - secure: "A+Ej5Xa/BKWkcGl1DSWTZCvchaanKE0/7NuPnNtT+PA4xVoM4w8Rj4e4fBBclCcCH+y0hg4pkS8UptB7NjLVdXXn/ytFNcLj7asuaPxheOLIRddQ0fGEVpYeM3ZCU25Mb8LI1nQECpJMl1TE4HaxOVunfN7MSxo1SQ0GlQ98YGo="
         # DOCKER_PASS (for Quay.io)
-        - secure: ZrX/Hq6T3X1Nw83+wjoAia9h6g00o8hV/dJAONnWYflpeSc16AKs8d4bBKPxE+rW+8I8JzoUWpdgN9Zq87+Vd3la8V4S1NCw7iZFYshzOZIbXtJZIC18NqsWDL5Kg0Ud08Y5GlI14Rjyc/zWmn5LmAHbZLk9EudtrcUmUmce1Ek=
+        - secure: "V+2MVaKXpMdno91MIF8fTqsRORT4GyheeVXzjVSC28IlyMntGe5N0wBI0nC/NdfQD3DH7MYRltDH/CgE2kcu1tWNGQK9hupClBzxz2X++md995DeyV+fTdkVnsQIYIrLfq/Lw0PuO3gYX7UATur1jevewpf+LbL7/Ar2mYE2pgY="
         ## DOCKER_USER_MIRROR (for DockerHub)
-        - secure: NErgcpFHK3Q51idZumScyRlr6PJjuFirHXlJJSPFhtKBh1Gg+z2Z3DLoFCOTibIyJSVo38T2eA53daM3VmPWb3kd4brrLjjoH7a3i/838IJjIDLpFULAc3uzP7PGckEiXb8gB1lQB/IaeDiWWUL2SbzMOdLABpANpR1AYmF00VI=
+        - secure: "cEf0IdgJapIVX+rchN/Q+PgCYFXmUjfBBATlOt6KSQfozGc3YvT8BxtIaRj5v+fARc/gymBPfy2ZWfaLG9jWMdbjML7NIfMl2gRAHDuJSerl6xlYWrioIPe0zs7pBPT0JyRjqi0Gt9VJltn6CUBSbqK32TheLAKA1YJJqWoQOWo="
         ## DOCKER_PASS_MIRROR (for DockerHub)
-        - secure: PGfcYRtbZJSa09ZPGguBWyZAiUBnRkQRgowg3qasK4hT2vlhXOqgSmQNwRHHbUZA7d/s11u6Q4732L1+JnelnFc9yDTVDguawvM9ENrDYjDe4bZPMqbxsUWOCSPSd8JSjvcOtg+BLGhzmwxYFIRl5jOoS8Wkvos1fRpKbYNRY20=
+        - secure: "Vzm7gwu/h1Gg8wg4ulYipSmdW0BMT7n0DIi8Pf6AgNFle1dvW7/LC21rHOQbI+ClJj7nV9v/Qv/nkbpbH7XmJ/F/dW5B7mf07mmk2VR+Ncl0ThOEsSWBQF6Md4HTnU3fUREvTxY17AgMjSKx6ErppirNetmnmJ4Ogcusv4N33Fo="
         # DX_API_TOKEN (for DNAnexus builds)
-        - secure: RENKuendRiAmWxn+lgGF+XXPUHzfRDHGUaP4uR5mpnKOqGKVZX3uadFv/w1POuyxIR7QEt0EcgtbjJYsvEioyQRwsYQe9f1ekQU1k6+cyPS/eDqvwciXA2M+yqjNdAafQu4drN+aNV7qC8ZEU0MZXk3IaItB4g8z5ZfxfM54+m0=
+        - secure: "BnUw6ceEClSBFJjZgCy6GebD1ENxaHp3En05maWExdx0xyCb+T09XM1BrsCpPOv25npVUt8Q/YB6YpAiSGMT+RUwdiGj4OtaJb+I3HY/2fT1P7eCIEVITQhtGy5e/vFnavSk0eKzCV09z94c1kqjG3JnTocpPUa1W3JBxVr96vs="
         - DX_PROJECT=project-F8PQ6380xf5bK0Qk0YPjB17P
       install:
         #- travis/upgrade-docker.sh
@@ -106,7 +106,7 @@ jobs:
     #  env:
     #    - TRAVIS_JOB=build_dxWDL
     #    # DX_API_TOKEN (for DNAnexus builds)
-    #    - secure: laEq3qUZr6Dmvv1RvwvapNRNFxbWubkmGGmAqw/v1o8BcHuIL6lSvz2fZnvlMK8J8ySfL/4tawsgIU7bnh3H57u9bZdR37pNZthZ+4jguegKg8R5dpCxftEQRkgNN1C2LdTzkOYZvXq6i7tXHiDUJN2aWeElf6UDqspdbSFM+L0=
+    #    - secure: "IPvLIQudIRyUl8iLNLujDig1afV+2v8AtRHpw0LsbL45xr0TvkmqjoHRmkYDnbdEeVdGC91ydLwfLNXcU/Cn7KRuIPE3InYX6VeomVO87aIXUzmmBCdFNGKd6o0u6Q/T+oJxemXwztW9XpKx3yT4RdLj7/zEpXnJm07/mKiquZE="
     #    - DX_PROJECT=project-F856jv809y3VkzyFGkKqX367
     #  install:
     #    - travis/install-wdl.sh
@@ -143,7 +143,7 @@ jobs:
       env:
         - TRAVIS_JOB=build_conda
         # $ANACONDA_TOKEN for uploading builds to anaconda.org ("broad-viral" channel)
-        - secure: SLPB86BpMIiNncMioxVk9cLrqaSNt8F1QDtxkrdLq9j7wXzFqGa7cipG6UJ6Om7GvoF49DpACfGPTA4ycr+T4cH3pWXpBHrBhV8TyKJb23cOmg5+7zqJQTzuwNqKOT7t9rnBkf1uzVXBcgqKaD6XW/nEvNFK00I0cvjlCp8vgxE=
+        - secure: "cDKRuVUr2NMZk933RHMMYKDCfU2gZfe3VJLNG82zsj47rrfoRzUsDny71v27OuydgjICiBWGuFAl4alNBVkzQWGt7G1DaFVLn48SwqtnG4u0KAUVX32b/0sw7OrXRDDqD5pr5Q8J59xwxSKQmmXFXlMbZpSEeREf8c3Yn6pvm2c="
       install:
         - source travis/install-conda.sh
         - travis/install-conda-build.sh
@@ -230,7 +230,7 @@ jobs:
     #  env:
     #    - TRAVIS_JOB=build_conda_in_docker
     #    # $ANACONDA_TOKEN for uploading builds to anaconda.org ("broad-viral" channel)
-    #    - secure: SLPB86BpMIiNncMioxVk9cLrqaSNt8F1QDtxkrdLq9j7wXzFqGa7cipG6UJ6Om7GvoF49DpACfGPTA4ycr+T4cH3pWXpBHrBhV8TyKJb23cOmg5+7zqJQTzuwNqKOT7t9rnBkf1uzVXBcgqKaD6XW/nEvNFK00I0cvjlCp8vgxE=
+    #    - secure: "cDKRuVUr2NMZk933RHMMYKDCfU2gZfe3VJLNG82zsj47rrfoRzUsDny71v27OuydgjICiBWGuFAl4alNBVkzQWGt7G1DaFVLn48SwqtnG4u0KAUVX32b/0sw7OrXRDDqD5pr5Q8J59xwxSKQmmXFXlMbZpSEeREf8c3Yn6pvm2c="
     #  install:
     #    - DOCKER_TAG=`travis/list-docker-tags.sh | tail -1`
     #    - docker pull $DOCKER_TAG

DEVELOPMENT_NOTES.md

@@ -23,7 +23,7 @@ When upgrading the GATK to a new version:
 - in docker/rundocker.sh 
 
 ### (Automated) testing 
-[Travis CI](https://travis-ci.org/broadinstitute/viral-ngs) performs automated unit and integration tests for viral-ngs on each branch and pull request. Unit tests are run on each new branch commit, and longer integration tests are performed on pull requests to help ensure the stability of the `master` branch. Pull requests are gated to ensure merging to `master` is allowed only if all tests pass. The Travis configuration is specified in `.travis.yml`, and relies on files stored within `viral-ngs/travis/`.
+[Travis CI](https://travis-ci.com/broadinstitute/viral-ngs) performs automated unit and integration tests for viral-ngs on each branch and pull request. Unit tests are run on each new branch commit, and longer integration tests are performed on pull requests to help ensure the stability of the `master` branch. Pull requests are gated to ensure merging to `master` is allowed only if all tests pass. The Travis configuration is specified in `.travis.yml`, and relies on files stored within `viral-ngs/travis/`.
 
 A few notes on testing: 
 - Travis Linux with Py3 is the authoritative test server

README.md

@@ -1,6 +1,6 @@
 [![Docker Repository on Quay](https://quay.io/repository/broadinstitute/viral-ngs/status "Docker Repository on Quay")](https://quay.io/repository/broadinstitute/viral-ngs)
 [![broad-viral-badge](https://img.shields.io/badge/install%20from-broad--viral-green.svg?style=flat-square)](https://anaconda.org/broad-viral/viral-ngs)
-[![Build Status](https://travis-ci.org/broadinstitute/viral-ngs.svg?branch=master)](https://travis-ci.org/broadinstitute/viral-ngs)
+[![Build Status](https://travis-ci.com/broadinstitute/viral-ngs.svg?branch=master)](https://travis-ci.com/broadinstitute/viral-ngs)
 [![Coverage Status](https://coveralls.io/repos/broadinstitute/viral-ngs/badge.png)](https://coveralls.io/r/broadinstitute/viral-ngs)
 [![Code Health](https://landscape.io/github/broadinstitute/viral-ngs/master/landscape.svg?style=flat)](https://landscape.io/github/broadinstitute/viral-ngs)
 [![Documentation Status](https://readthedocs.org/projects/viral-ngs/badge/?version=latest)](http://viral-ngs.readthedocs.io/en/latest/?badge=latest)

travis/trigger-travis.sh

@@ -13,7 +13,7 @@
 # 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 --pro means to use travis-ci.com instead of travis-ci.com, and
 # where TRAVIS_ACCESS_TOKEN is, or ~/private/.travis-access-token contains,
 # the Travis access token.
 #
@@ -25,16 +25,16 @@
 #    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 .
+# Travis token available at https://travis-ci.com/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
+#   https://travis-ci.com/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/.
+# the job, but won't be visible to anyone browsing https://travis-ci.com/.
 #
 # 2. Add the following before_install and after_script block to your
 # .travis.yml file, where you replace OTHERGITHUB* by a specific downstream
@@ -113,7 +113,7 @@ if [ "$1" = "--pro" ] ; then
   TRAVIS_URL=travis-ci.com
   shift
 else
-  TRAVIS_URL=travis-ci.org
+  TRAVIS_URL=travis-ci.com
 fi
 
 if [ "$1" = "--branch" ] ; then