Commit 4cee6703 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 3.0~beta3+dfsg

parent c247b762

.travis.yml

+35 −12
Original line number Diff line number Diff line
@@ -6,12 +6,9 @@ addons: 
  apt:

    packages:

    - cmake

language: cpp



before_install:

- git submodule update --init --recursive

- test -n $CC  && unset CC

- test -n $CXX && unset CXX



script:

- mkdir build
@@ -30,7 +27,7 @@ matrix: 
          packages:

            - g++-4.9

            - mpi-default-dev

      env: COMPILER=g++-4.9

      env: CXX=g++-4.9

    - compiler: gcc

      addons:

        apt:
@@ -39,7 +36,7 @@ matrix: 
          packages:

            - g++-5

            - mpi-default-dev

      env: COMPILER=g++-5

      env: CXX=g++-5

    - compiler: gcc

      addons:

        apt:
@@ -48,7 +45,16 @@ matrix: 
          packages:

            - g++-6

            - mpi-default-dev

      env: COMPILER=g++-6

      env: CXX=g++-6

    - compiler: gcc

      addons:

        apt:

          sources:

            - ubuntu-toolchain-r-test

          packages:

            - g++-7

            - mpi-default-dev

      env: CXX=g++-7

    - compiler: clang

      addons:

        apt:
@@ -58,7 +64,7 @@ matrix: 
          packages:

            - clang-3.6

            - mpi-default-dev

      env: COMPILER=clang++-3.6

      env: CXX=clang++-3.6

    - compiler: clang

      addons:

        apt:
@@ -68,7 +74,7 @@ matrix: 
          packages:

            - clang-3.7

            - mpi-default-dev

      env: COMPILER=clang++-3.7

      env: CXX=clang++-3.7

    - compiler: clang

      addons:

        apt:
@@ -78,7 +84,24 @@ matrix: 
          packages:

            - clang-3.8

            - mpi-default-dev

      env: COMPILER=clang++-3.8





      env: CXX=clang++-3.8

    - compiler: clang

      addons:

        apt:

          sources:

            - ubuntu-toolchain-r-test

            - llvm-toolchain-trusty-3.9

          packages:

            - clang-3.9

            - mpi-default-dev

      env: CXX=clang++-3.9

    - compiler: clang

      addons:

        apt:

          sources:

            - ubuntu-toolchain-r-test

            - llvm-toolchain-trusty-4.0

          packages:

            - clang-4.0

            - mpi-default-dev

      env: CXX=clang++-4.0

CMakeLists.txt

+20 −1
Original line number Diff line number Diff line
@@ -19,6 +19,25 @@ elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel") 
  set(CMAKE_COMPILER_IS_ICC 1)

endif()





message("-- Processor is ${CMAKE_SYSTEM_PROCESSOR}")



if(CMAKE_SYSTEM_PROCESSOR MATCHES "amd64.*|x86_64.*|AMD64.*")

  set(X86_64 1)

elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "i686.*|i386.*|x86.*|amd64.*|AMD64.*")

  set(X86 1)

elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^(arm.*|ARM.*)")

  set(ARM 1)

elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^(aarch64.*|AARCH64.*)")

  set(AARCH64 1)

elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "PPC64*|ppc64*|powerpc64*")

  set(PPC64 1)

elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "PPC*|ppc*|powerpc*")

  set(PPC 1)

endif()







set (HHSUITE_VERSION_MAJOR 3)

set (HHSUITE_VERSION_MINOR 0)

set (HHSUITE_VERSION_PATCH 0)
@@ -39,12 +58,12 @@ INSTALL(FILES 
include_directories(src)

include_directories(lib/ffindex/src)



add_subdirectory(lib/ffindex)

add_subdirectory(src)

add_subdirectory(data)

add_subdirectory(scripts)

add_subdirectory(test)

#add_subdirectory(doc)

add_subdirectory(lib/ffindex)





SET (CPACK_GENERATOR "DEB;TGZ;ZIP;RPM")

README

+1 −0
Original line number Diff line number Diff line
@@ -16,6 +16,7 @@ For full documentation see the user guide in hhsuite-userguide.pdf 
To compile from source, you will need:

 * a recent C/C++ compiler

 * CMake 2.8.12 or later

 * pdbx python library for example from https://github.com/soedinglab/pdbx



*****************************************************************************

2. Installation

README.md

+8 −0
Original line number Diff line number Diff line
@@ -10,12 +10,20 @@ 


The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).



## WARNING ##

We had to rename our repository for ffindex, so it might be necessary to run the following commands to update the submodule in your clone:



	git pull

	git submodule deinit

	git submodule init





## Requirements



To compile from source, you will need:

 * a recent C/C++ compiler

 * [CMake](http://cmake.org/) 2.8.12 or later

 * install [pdbx python library](https://github.com/soedinglab/pdbx)





## Installation

doc/hhsuite-userguide.tex

+227 −17

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