Use mmseqs modularization in plass

.github/ISSUE_TEMPLATE.md

@@ -5,16 +5,16 @@
## Steps to Reproduce (for bugs)
Please make sure to execute the reproduction steps with newly recreated and empty tmp folders.

## MMseqs Output (for bugs)
Please make sure to also post the complete output of MMseqs. You can use gist.github.com for large output.
## Plass Output (for bugs)
Please make sure to also post the complete output of Plass. You can use gist.github.com for large output.

## Context
Providing context helps us come up with a solution and improve our documentation for the future.

## Your Environment
Include as many relevant details about the environment you experienced the bug in.
* Git commit used (The string after "MMseqs Version:" when you execute MMseqs without any parameters):
* Which MMseqs version was used (Statically-compiled, self-compiled, Homebrew, etc.):
* Git commit used (The string after "Plass Version:" when you execute Plass without any parameters):
* Which Plass version was used (Statically-compiled, self-compiled, Homebrew, etc.):
* For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation:
* Server specifications (especially CPU support for AVX2/SSE and amount of system memory):
* Operating system and version:

.gitmodules

@@ -0,0 +1,3 @@
[submodule "lib/mmseqs"]
	path = lib/mmseqs
	url = https://github.com/soedinglab/MMseqs2.git

CMakeLists.txt

@@ -1,66 +1,12 @@
cmake_minimum_required(VERSION 2.8.12 FATAL_ERROR)
project(MMseqs CXX)
message("-- Source Directory: ${CMAKE_CURRENT_SOURCE_DIR}")
message("-- Project Directory: ${PROJECT_SOURCE_DIR}")
cmake_minimum_required(VERSION 2.8.9 FATAL_ERROR)
project(plass CXX)
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_CURRENT_SOURCE_DIR}/lib/mmseqs/cmake")

set(FRAMEWORK_ONLY 0 CACHE BOOL "Framework Mode")
set(HAVE_SANITIZER 0 CACHE BOOL "Have Sanitizers")
set(VERSION_OVERRIDE "" CACHE STRNG "Override version string in help and usage messages")

#Sanitizers
if (${HAVE_SANITIZER})
    include(FindUBSan)
    include(FindASan)
    include(FindMSan)
    include(FindTSan)
endif ()

if (NOT CMAKE_BUILD_TYPE)
    set(CMAKE_BUILD_TYPE Release)
endif (NOT CMAKE_BUILD_TYPE)

# find compiler
if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
    # using Clang
    message("-- Compiler is clang(++)")
    set(CMAKE_COMPILER_IS_CLANG 1)
elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
    # using GCC
    message("-- Compiler is GNU ")
    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS "4.6.0")
        message(FATAL_ERROR "Insufficient gcc version")
    endif ()
elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
    # using Intel C++
    message("-- Compiler is icc(++)")
    set(CMAKE_COMPILER_IS_ICC 1)
endif ()

# set flags
set(MMSEQS_CXX_FLAGS "-std=c++0x -m64")

# Compiler-specific features
if (CMAKE_COMPILER_IS_CLANG)
    set(CMAKE_XCODE_ATTRIBUTE_CLANG_CXX_LANGUAGE_STANDARD "c++11")
    set(CMAKE_XCODE_ATTRIBUTE_CLANG_CXX_LIBRARY "libc++")
    set(MMSEQS_CXX_FLAGS "${MMSEQS_CXX_FLAGS} -stdlib=libc++")
endif ()

set(FRAMEWORK_ONLY 1 CACHE INTERNAL "" FORCE)
include(MMseqsSetupDerivedTarget)
add_subdirectory(lib/mmseqs)
add_subdirectory(data)
include_directories(lib)
include_directories(lib/kseq)
include_directories(lib/simd)
include_directories(lib/gzstream)
include_directories(lib/alp)
include_directories(lib/cacode)
include_directories(lib/ksw2)
include_directories(lib/kerasify)
add_subdirectory(lib/kerasify)
add_subdirectory(lib/cacode)
add_subdirectory(lib/alp)
add_subdirectory(lib/ksw2)
add_subdirectory(data)
add_subdirectory(src)
if (NOT FRAMEWORK_ONLY)
    add_subdirectory(util)
endif ()

Dockerfile

@@ -1,24 +1,17 @@
FROM alpine:latest as mmseqs-builder
FROM alpine:latest AS plass-builder

RUN apk add --no-cache gcc g++ cmake musl-dev vim git ninja zlib-dev bzip2-dev
RUN apk add --no-cache gcc g++ cmake musl-dev git ninja 

WORKDIR /opt/mmseqs
WORKDIR /opt/plass
ADD . .

RUN git submodule init && git submodule update

WORKDIR build_sse
RUN cmake -G Ninja -DHAVE_SSE4_1=1 -DHAVE_MPI=0 -DHAVE_TESTS=0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..
RUN cmake -G Ninja -DHAVE_SSE=1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..
RUN ninja && ninja install

WORKDIR ../build_avx
RUN cmake -G Ninja -DHAVE_AVX2=1 -DHAVE_MPI=0 -DHAVE_TESTS=0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..
RUN cmake -G Ninja -DHAVE_AVX=1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..
RUN ninja && ninja install

FROM alpine:latest
MAINTAINER Milot Mirdita <milot@mirdita.de>
RUN apk add --no-cache gawk bash grep libstdc++ libgomp zlib libbz2

COPY --from=mmseqs-builder /opt/mmseqs/build_sse/bin/mmseqs /usr/local/bin/mmseqs_sse42
COPY --from=mmseqs-builder /opt/mmseqs/build_avx/bin/mmseqs /usr/local/bin/mmseqs_avx2
ADD util/mmseqs_wrapper.sh /usr/local/bin/mmseqs

CMD ["mmseqs"]