Commit 46a2d2a0 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.0.0

parent 142f48e4

.travis.yml

+43 −56
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sudo: required

dist: trusty

sudo: false

language: cpp

before_install:

 - test $(uname) = "Linux" && sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test || true

 - test $(uname) = "Linux" && sudo add-apt-repository -y ppa:george-edison55/cmake-3.x || true

 - test $(uname) = "Linux" && sudo add-apt-repository -y 'deb http://llvm.org/apt/trusty/ llvm-toolchain-trusty-3.8 main' || true

 - test $(uname) = "Linux" && sudo add-apt-repository -y 'deb http://llvm.org/apt/trusty/ llvm-toolchain-trusty-3.9 main' || true

 - test $(uname) = "Linux" && wget -O - http://llvm.org/apt/llvm-snapshot.gpg.key | sudo apt-key add - || true

 - test $(uname) = "Linux" && sudo apt-get update -y || true

 - test $(uname) = "Linux" && sudo apt-get install -qq -y g++-4.9 g++-5 g++-6 clang-3.8 clang-3.9 cmake cmake-data zlib1g-dev libbz2-dev || true

 - test $(uname) = "Darwin" && brew update || true

 - test $(uname) = "Darwin" && brew install gcc@4.9 || true

 #- test $(uname) = "Darwin" && brew install gcc@5 || true

 #- test $(uname) = "Darwin" && brew install gcc@6 || true

 - test $(uname) = "Darwin" && brew install gcc || true

matrix:

  include:

    - os: linux

      compiler: gcc-4.9

      addons:

        apt:

          sources: ['ubuntu-toolchain-r-test']

          packages: ['g++-4.9', 'cmake', 'cmake-data', 'zlib1g-dev', 'libbz2-dev', 'libboost-dev', 'python', 'python-nose', 'python-jinja2', 'python-pip']

      install: export CXX="g++-4.9"

      env: CMAKE_ARGS="-DLAMBDA_STATIC_BUILD=1"



    - os: linux

      compiler: gcc-5

      addons:

        apt:

          sources: ['ubuntu-toolchain-r-test']

          packages: ['g++-5', 'cmake', 'cmake-data', 'zlib1g-dev', 'libbz2-dev', 'libboost-dev', 'python', 'python-nose', 'python-jinja2', 'python-pip']

      install: export CXX="g++-5"

      env: CMAKE_ARGS="-DCMAKE_BUILD_TYPE=RelWithDebInfo"

    - os: linux

      compiler: gcc-6

      install: export CXX="g++-6"

      env: CMAKE_ARGS="-DLAMBDA_MULTIOPT_BUILD=1"



    - os: linux

      compiler: clang-3.8

      install: export CXX="clang++-3.8"

      compiler: gcc-7

      addons:

        apt:

          sources: ['ubuntu-toolchain-r-test']

          packages: ['g++-7', 'cmake', 'cmake-data', 'zlib1g-dev', 'libbz2-dev', 'libboost-dev', 'python', 'python-nose', 'python-jinja2', 'python-pip']

      install: export CXX="g++-7"

      env: CMAKE_ARGS="-DCMAKE_CXX_FLAGS=-std=c++17"



    - os: linux

      compiler: clang-3.9

      addons:

        apt:

          sources: ['ubuntu-toolchain-r-test', 'llvm-toolchain-trusty-3.9']

          packages: ['clang-3.9', 'g++-7', 'cmake', 'cmake-data', 'zlib1g-dev', 'libbz2-dev', 'libboost-dev', 'python', 'python-nose', 'python-jinja2', 'python-pip'] # g++ required for newer libstdc++

      install: export CXX="clang++-3.9"



    - os: linux

      compiler: clang-5

      addons:

        apt:

          sources: ['ubuntu-toolchain-r-test']

          packages: ['g++-7', 'cmake', 'cmake-data', 'zlib1g-dev', 'libbz2-dev', 'libboost-dev', 'python', 'python-nose', 'python-jinja2', 'python-pip'] # g++ required for newer libstdc++

      install: export CXX="/usr/local/clang-5.0.0/bin/clang++"

      env: CMAKE_ARGS="-DCMAKE_BUILD_TYPE=RelWithDebInfo" LD_LIBRARY_PATH="/usr/local/clang-5.0.0/lib/:${LD_LIBRARY_PATH}"



    - os: osx

      compiler: gcc-4.9

      before_install:

        - brew update

        - brew install gcc@4.9

      install: export CXX="g++-4.9"

      env: CMAKE_ARGS="-DLAMBDA_FASTBUILD=1 -DLAMBDA_STATIC_BUILD=1"

    #- os: osx

      #compiler: gcc-5

      #install: export CXX="g++-5"

      #env: CMAKE_ARGS="-DLAMBDA_FASTBUILD=1"

    #- os: osx

      #compiler: gcc-6

      #install: export CXX="g++-6"

      #env: CMAKE_ARGS="-DLAMBDA_FASTBUILD=1"



    - os: osx

      compiler: gcc-7

      before_install:

        - brew update

        - brew install gcc@7

      install: export CXX="g++-7"

      env: CMAKE_ARGS="-DLAMBDA_FASTBUILD=1"



    #- os: osx

      #compiler: clang-3.6

      #before_install:

        #- sudo brew update

        #- sudo brew tap homebrew/versions

        #- sudo brew install llvm36

      #install: ['export CXX="clang++-3.6"' ]



    #- os: osx

      #compiler: clang-3.7

      #before_install:

        #- sudo brew update

        #- sudo brew tap homebrew/versions

        #- sudo brew install llvm37

      #install: ['export CXX="clang++-3.7"' ]



    #- os: osx

      #compiler: clang-3.8

      #before_install:

        #- sudo brew update

        #- sudo brew tap homebrew/versions

        #- sudo brew install llvm38

      #install: export CXX="clang++-3.8" CMAKE_ARGS='-DLAMBDA_NATIVE_BUILD=0 -DLAMBDA_FASTBUILD=1 -DCMAKE_CXX_FLAGS="-L/usr/local/Cellar/llvm38/3.8.0/lib/llvm-3.8/lib"'



script:

  - mkdir -p build && cd build

  - cmake .. -DLAMBDA_NATIVE_BUILD=0 ${CMAKE_ARGS}

  - make lambda_indexer VERBOSE=1

  - travis_wait make lambda VERBOSE=1 # need to prefix with travis_wait because it might take > 10min

  - cmake .. -DLAMBDA_NATIVE_BUILD=0 -DLAMBDA_COMPILE_THREADS=2 ${CMAKE_ARGS}

  - travis_wait make VERBOSE=1 # need to prefix with travis_wait because it might take > 10min

  - ctest .

CMakeLists.txt

+6 −3
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@@ -10,7 +10,7 @@ set(ColourRed "${Esc}[31m") 


message ("${ColourBold}Compiler Detection${ColourReset}")



project (lambda CXX)

project (lambda2 CXX)



# ----------------------------------------------------------------------------

# Make "Release" the default cmake build type
@@ -32,6 +32,9 @@ if (EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/include/seqan/include/seqan/version.h") 
    set (CMAKE_INCLUDE_PATH

        ${CMAKE_CURRENT_SOURCE_DIR}/include/seqan/include

        ${CMAKE_INCLUDE_PATH})

    set (CMAKE_PREFIX_PATH

        ${CMAKE_CURRENT_SOURCE_DIR}/include/seqan/util/cmake

        ${CMAKE_PREFIX_PATH})

    set (CMAKE_MODULE_PATH

        ${CMAKE_CURRENT_SOURCE_DIR}/include/seqan/util/cmake

        ${CMAKE_MODULE_PATH})
@@ -57,5 +60,5 @@ endif () 
# Add Tests

# ----------------------------------------------------------------------------



message ("\n${ColourBold}Setting up unit tests${ColourReset}")

add_subdirectory(tests)
 
# message ("\n${ColourBold}Setting up unit tests${ColourReset}")

# add_subdirectory(tests)

INFO

+2 −2
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Name: lambda

Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>

Maintainer: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>

License: GPL v3

Copyright: 2013-2017, Hannes Hauswedell; 2016-2017 Knut Reinert, FU-Berlin

License: AGPL v3

Copyright: 2013-2019, Hannes Hauswedell; 2016-2019 Knut Reinert, FU-Berlin

Status: under development

Description: Lambda is a biological sequence aligner optimized for many

query sequences and searches in protein space. It is highly compatible

LICENSE-AGPL3.rst

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LICENSE-BSD.rst

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BSD-License (3-clause)

======================



 | Copyright (c) 2016-2017, Knut Reinert, Freie Universität Berlin

 | Copyright (c) 2016-2019, Knut Reinert, Freie Universität Berlin

 | All rights reserved.



Redistribution and use in source and binary forms, with or without