Merge pull request #917 from COMBINE-lab/develop

Develop

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 <SOURCE_DIR>/build"
-#    BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libdivsufsort-master/build
-#    CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR> -DBUILD_DIVSUFSORT64=TRUE -DUSE_OPENMP=TRUE -DBUILD_SHARED_LIBS=FALSE
-#  )
-#  externalproject_add_step(libdivsufsort makedir
-#    COMMAND mkdir -p <SOURCE_DIR>/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}"
@@ -785,26 +755,29 @@ 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)
   message("Build system will compile Staden IOLib")
   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 ${CMAKE_CURRENT_SOURCE_DIR}/external/install
     CONFIGURE_COMMAND ./configure --enable-shared=no --without-libcurl --prefix=<INSTALL_DIR> LDFLAGS=${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
   )

current_version.txt

@@ -1,3 +1,3 @@
 VERSION_MAJOR 1
 VERSION_MINOR 10
-VERSION_PATCH 2
+VERSION_PATCH 3

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.

docker/Dockerfile

@@ -6,7 +6,7 @@ MAINTAINER [email protected]
 
 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
 

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 .

include/SalmonConfig.hpp

@@ -1,10 +1,10 @@
 /**
 >HEADER
-    Copyright (c) 2014-2022 Rob Patro [email protected]
+    Copyright (c) 2014-2024 Rob Patro [email protected]
 
     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

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