New upstream version 0.12.0+ds1

filter=-linelength

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echo "[Drone build] cmake configuration"

cmake -DDO_QUIET_MAKE=TRUE ..

cmake -DDO_QUIET_MAKE=TRUE -DBOOST_ROOT=/usr ..

echo "[Drone build] making salmon and installing locally (this could take a while)"

---

name: Bug report

about: Create a report to help us improve

---

**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?**

**Describe the bug**

A clear and concise description of what the bug is.

**To Reproduce**

Steps and data to reproduce the behavior:

Specifically, please provide at least the following information:

  * Which version of salmon was used?

  * How was salmon installed (compiled, downloaded executable, through bioconda)?

  * Which reference (e.g. transcriptome) was used?

  * Which read files were used?

  * Which which program options were used?

**Expected behavior**

A clear and concise description of what you expected to happen.

**Screenshots**

If applicable, add screenshots or terminal output to help explain your problem.

**Desktop (please complete the following information):**

 - OS: [e.g. Ubuntu Linux, OSX]

 - Version [ If you are on OSX, the output of `sw_vers`. If you are on linux the output of `uname -a` and `lsb_release -a`]

**Additional context**

Add any other context about the problem here.

#whitelist

branches:

    only:

        - master

        - develop

language: cpp

compiler: gcc

before_install:

    - echo "yes" | sudo apt-add-repository ppa:boost-latest

    - echo "yes" | sudo apt-add-repository ppa:mapnik/boost-backports-1-54

    - echo "yes" | sudo apt-add-repository ppa:h-rayflood/gcc-upper

    - sudo apt-get clean -qq

    - sudo apt-get update -qq

    - sudo apt-get install -qq gcc-4.9 g++-4.9 

    - export CC="gcc-4.9"

    - export CXX="gcc-4.9"

    - sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 50

    - sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.9 50

dist: trusty

sudo: false

git:

  depth: 1

language: generic

matrix:

  include:

    - env: CC=gcc-7 CXX=g++-7 AR=gcc-ar-7 NM=gcc-nm-7 RANLIB=gcc-ranlib-7

    - env: CC=gcc-5 CXX=g++-5 AR=gcc-ar-5 NM=gcc-nm-5 RANLIB=gcc-ranlib-5

    - language: python

      python: "3.6"

      name: Lint cmake files.

      install: pip3 install cmakelint

      script: scripts/lint.sh

  allow_failures:

    - name: Lint cmake files.

  fast_finish: true

install:

    - export CXX="g++-4.9"

    - export CC="gcc-4.9"

  # https://launchpad.net/~ubuntu-toolchain-r/+archive/ubuntu/test

  - sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test

  - sudo apt-get update -qq

  - sudo apt-get install -qq zlib1g-dev libbz2-dev cmake

  - |

    if [[ "${CC}" =~ gcc- ]]; then

      echo "Installing ${CC}."

      sudo apt-get install -qq "${CC}"

    fi

  - |

    if [[ "${CXX}" =~ g\+\+- ]]; then

      echo "Installing ${CXX}."

      sudo apt-get install -qq "${CXX}"

    fi

script:

  - LD_LIBRARY_PATH=${TRAVIS_BUILD_DIR}/lib:$LD_LIBRARY_PATH

  - mkdir build

    - cd build 

    - cmake -DFETCH_BOOST=TRUE -DNO_RTM=TRUE .. 

    - travis_wait 45 make 

    - travis_wait make install

    - travis_wait make test VERBOSE=1

  - pushd build

  # Set make -j N considering Travis providing 2 cores.

  # VERBOSE=1 to show the input commands in generatd Makefile for debug.

  - |

    cmake \

      -DFETCH_BOOST=TRUE \

      -DNO_RTM=TRUE \

      .. && \

    make -j 4 VERBOSE=1 && \

    make install && \

    ./src/salmon -h

  - |

    make CTEST_OUTPUT_ON_FAILURE=1 VERBOSE=1 test

  - popd

after_success:

    - cd $TRAVIS_BUILD_DIR

  - ./scripts/push-binary.sh

after_failure:

    - cat $TRAVIS_BUILD_DIR/build/Testing/Temporary/LastTest.log

  - echo "Failure"

  - ls -laR $TRAVIS_BUILD_DIR/build/Testing/

  - cat $TRAVIS_BUILD_DIR/build/Testing/Temporary/*