diff --git a/CMakeLists.txt b/CMakeLists.txt index aa9257bf1..0ff9550f9 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -428,7 +428,7 @@ endif() ## # Set the latest version and look for what we need ## -set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0" "1.72.0" "1.73.0" "1.74.0" "1.75.0" "1.76.0" "1.77.0" "1.78.0") +set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0" "1.72.0" "1.73.0" "1.74.0" "1.75.0" "1.76.0" "1.77.0" "1.78.0" "1.79.0" "1.80.0" "1.81.0" "1.82.0" "1.83.0" "1.84.0") if (NOT BOOST_RECONFIGURE) find_package(Boost 1.59.0 COMPONENTS iostreams system filesystem timer chrono program_options) message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}") @@ -548,38 +548,6 @@ message("BOOST LIBRARIES = ${Boost_LIBRARIES}") set(EXTERNAL_LIBRARY_PATH $CMAKE_CURRENT_SOURCE_DIR/lib) -#find_package(libdivsufsort) -#if(NOT LIBDIVSUFSORT_FOUND) -# message("Build system will build libdivsufsort") -# message("==================================================================") -# include(ExternalProject) -# externalproject_add(libdivsufsort -# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -# URL ${CMAKE_CURRENT_SOURCE_DIR}/external/libdivsufsort.zip -# # Note: This zip comes from the fetched rapmap.zip, whose SHA we check -# # so we souldn't need to check this one separately. -# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libdivsufsort-master -# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install -# #UPDATE_COMMAND sh -c "mkdir -p /build" -# BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libdivsufsort-master/build -# CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH= -DBUILD_DIVSUFSORT64=TRUE -DUSE_OPENMP=TRUE -DBUILD_SHARED_LIBS=FALSE -# ) -# externalproject_add_step(libdivsufsort makedir -# COMMAND mkdir -p /build -# COMMENT "Make build directory" -# DEPENDEES download -# DEPENDERS configure) -# -# set(SUFFARRAY_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include) -# set(FETCHED_LIBDIVSUFSORT TRUE) -#else() -# message("SUFFARRAY_LIB = ${SUFFARRAY_LIBRARY}") -# set(SUFFARRAY_LIB ${SUFFARRAY_LIBRARY}) -# message("SUFFARRAY_LIB64 = ${SUFFARRAY_LIBRARY64}") -# set(SUFFARRAY_LIB64 ${SUFFARRAY_LIBRARY64}) -# set(SUFFARRAY_INCLUDE_DIRS ${SUFFARRAY_INCLUDE_DIR}) -#endif() - find_package(cereal "1.3.2") if (NOT CEREAL_FOUND) message("Build system will fetch and build the cereal serialization library") @@ -642,7 +610,7 @@ endif() message("Build system will fetch and build Intel Threading Building Blocks") message("==================================================================") # These are useful for the custom install step we'll do later -set(TBB_SOURCE_DIR ${GAT_SOURCE_DIR}/external/oneTBB-2021.9.0) +set(TBB_SOURCE_DIR ${GAT_SOURCE_DIR}/external/oneTBB-2021.11.0) set(TBB_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install) if("${TBB_COMPILER}" STREQUAL "gcc") @@ -653,11 +621,13 @@ endif() set(TBB_CXXFLAGS "${TBB_CXXFLAGS} ${CXXSTDFLAG} ${SCHAR_FLAG}") + + ExternalProject_Add(libtbb DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -DOWNLOAD_COMMAND curl -k -L https://github.com/oneapi-src/oneTBB/archive/refs/tags/v2021.9.0.tar.gz -o v2021.9.tar.gz && -${SHASUM} 1ce48f34dada7837f510735ff1172f6e2c261b09460e3bf773b49791d247d24e v2021.9.tar.gz && -tar -xzvf v2021.9.tar.gz +DOWNLOAD_COMMAND curl -k -L https://github.com/oneapi-src/oneTBB/archive/refs/tags/v2021.11.0.tar.gz -o v2021.11.0.tar.gz && +${SHASUM} 782ce0cab62df9ea125cdea253a50534862b563f1d85d4cda7ad4e77550ac363 v2021.11.0.tar.gz && +tar -xzvf v2021.11.0.tar.gz SOURCE_DIR ${TBB_SOURCE_DIR} INSTALL_DIR ${TBB_INSTALL_DIR} PATCH_COMMAND "${TBB_PATCH_STEP}" @@ -785,7 +755,7 @@ find_package(CURL) if (FETCH_STADEN) set(LIBSTADEN_FOUND FALSE) else () - find_package(libstadenio 1.14.15) + find_package(libstadenio 1.15.0) endif() if (NOT LIBSTADENIO_FOUND) @@ -793,18 +763,21 @@ if (NOT LIBSTADENIO_FOUND) message("==================================================================") externalproject_add(libstadenio DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external - DOWNLOAD_COMMAND curl -k -L https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-14-15/io_lib-1.14.15.tar.gz -o staden-io_lib-v1.14.15.tar.gz && - ${SHASUM} 20814c4365e1e2fe6630fb11d0df370dec4c5688af3871de7f1cb0129671401e staden-io_lib-v1.14.15.tar.gz && - mkdir -p staden-io_lib-1.14.15 && - tar -xzf staden-io_lib-v1.14.15.tar.gz --strip-components=1 -C staden-io_lib-1.14.15 && + DOWNLOAD_COMMAND curl -k -L https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-15-0/io_lib-1.15.0.tar.gz -o staden-io_lib-v1.15.0.tar.gz && + ${SHASUM} ad343dac7c77086db1b54585c5887b26eda6430d1639d111dd3304c3b749494f staden-io_lib-v1.15.0.tar.gz && + mkdir -p staden-io_lib-1.15.0 && + tar -xzf staden-io_lib-v1.15.0.tar.gz --strip-components=1 -C staden-io_lib-1.15.0 && rm -fr staden-io_lib && - mv -f staden-io_lib-1.14.15 staden-io_lib + mv -f staden-io_lib-1.15.0 staden-io_lib && + curl -k -L https://github.com/samtools/htscodecs/releases/download/v1.6.0/htscodecs-1.6.0.tar.gz -o htscodecs-1.6.0.tar.gz && + mkdir -p htscodecs-1.6.0 && + tar -xzf htscodecs-1.6.0.tar.gz --strip-components=1 -C htscodecs-1.6.0 && + rm -fr staden-io_lib/htscodecs && + mv -f htscodecs-1.6.0 staden-io_lib/htscodecs SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install CONFIGURE_COMMAND ./configure --enable-shared=no --without-libcurl --prefix= LDFLAGS=${LIBSTADEN_LDFLAGS} CFLAGS=${LIBSTADEN_CFLAGS} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS+=${STADEN_INC} CFLAGS+=${STADEN_LIB} LDFLAGS+=${EXTRA_CMAKE_LIBRARY_FLAGS} CFLAGS+=${EXTRA_CMAKE_INCLUDE_FLAGS} CFLAGS+=${LZFLAG} CFLAGS+=${SCHAR_FLAG} - - BUILD_IN_SOURCE 1 INSTALL_COMMAND make install ) diff --git a/current_version.txt b/current_version.txt index df45a4964..0b9cdfaa5 100644 --- a/current_version.txt +++ b/current_version.txt @@ -1,3 +1,3 @@ VERSION_MAJOR 1 VERSION_MINOR 10 -VERSION_PATCH 2 +VERSION_PATCH 3 diff --git a/doc/source/conf.py b/doc/source/conf.py index 580dcefd3..2cd773765 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -57,7 +57,7 @@ # The short X.Y version. version = '1.10' # The full version, including alpha/beta/rc tags. -release = '1.10.2' +release = '1.10.3' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/docker/Dockerfile b/docker/Dockerfile index f79fe68f8..fc72d2cfa 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -6,7 +6,7 @@ MAINTAINER salmon.maintainer@gmail.com ENV PACKAGES git gcc make g++ libboost-all-dev liblzma-dev libbz2-dev \ ca-certificates zlib1g-dev libcurl4-openssl-dev curl unzip autoconf apt-transport-https ca-certificates gnupg software-properties-common wget -ENV SALMON_VERSION 1.10.2 +ENV SALMON_VERSION 1.10.3 # salmon binary will be installed in /home/salmon/bin/salmon diff --git a/docker/build_test.sh b/docker/build_test.sh index d700d7ed7..4e2690092 100644 --- a/docker/build_test.sh +++ b/docker/build_test.sh @@ -1,3 +1,3 @@ #! /bin/bash -SALMON_VERSION=1.10.2 +SALMON_VERSION=1.10.3 TMPDIR=/mnt/scratch7/DELETE_ME_TEMP docker build --no-cache -t combinelab/salmon:${SALMON_VERSION} -t combinelab/salmon:latest . diff --git a/include/SalmonConfig.hpp b/include/SalmonConfig.hpp index 7498c14b5..03a0ec925 100644 --- a/include/SalmonConfig.hpp +++ b/include/SalmonConfig.hpp @@ -1,10 +1,10 @@ /** >HEADER - Copyright (c) 2014-2022 Rob Patro rob@cs.umd.edu + Copyright (c) 2014-2024 Rob Patro rob@cs.umd.edu This file is part of Salmon. - Sailfish is free software: you can redistribute it and/or modify + Salmon is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. @@ -28,8 +28,8 @@ namespace salmon { constexpr char majorVersion[] = "1"; constexpr char minorVersion[] = "10"; -constexpr char patchVersion[] = "2"; -constexpr char version[] = "1.10.2"; +constexpr char patchVersion[] = "3"; +constexpr char version[] = "1.10.3"; constexpr uint32_t indexVersion = 5; constexpr char requiredQuasiIndexVersion[] = "p7"; } // namespace salmon diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh index bf2574e0f..95e300533 100755 --- a/scripts/fetchPufferfish.sh +++ b/scripts/fetchPufferfish.sh @@ -23,11 +23,11 @@ if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then rm -fr ${INSTALL_DIR}/src/pufferfish fi -SVER=salmon-v1.10.2 +SVER=salmon-v1.10.3 #SVER=develop #SVER=sketch-mode -EXPECTED_SHA256=f225b74833f71dcf767a565345224357fb091f90ce79717abc836814d9ccd101 +EXPECTED_SHA256=52b6699de0d33814b73edb3455175568c2330d8014be017dce7b564e54134860 mkdir -p ${EXTERNAL_DIR} curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip