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diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1be02ab..48ffda2 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -428,9 +428,9 @@ 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")
+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" "1.77.0" "1.78.0")
if (NOT BOOST_RECONFIGURE)
-find_package(Boost 1.59.0 COMPONENTS iostreams filesystem system timer chrono program_options)
+find_package(Boost 1.59.0 COMPONENTS ALL)
message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
message("Boost_FOUND = ${Boost_FOUND}")
@@ -610,7 +610,7 @@ if (NOT CEREAL_FOUND)
endif()
## Try and find TBB first
-find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
+find_package(TBB)
## NOTE: we actually require at least 2019 U4 or greater
## since we are using tbb::global_control. However, they
@@ -618,12 +618,8 @@ find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
## source. Check before release if we can bump to the 2020
## version (requires having tbb 2020 for OSX).
if (${TBB_FOUND})
- if (${TBB_VERSION} VERSION_GREATER_EQUAL 2019.0)
message("FOUND SUITABLE TBB VERSION : ${TBB_VERSION}")
set(TBB_TARGET_EXISTED TRUE)
- else()
- set(TBB_TARGET_EXISTED FALSE)
- endif()
else()
set(TBB_TARGET_EXISTED FALSE)
endif()
@@ -750,10 +746,6 @@ if(NOT libgff_FOUND)
message("Build system will compile libgff")
message("==================================================================")
externalproject_add(libgff
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -o libgff.tgz &&
- ${SHASUM} 7656b19459a7ca7d2fd0fcec4f2e0fd0deec1b4f39c703a114e8f4c22d82a99c libgff.tgz &&
- tar -xzvf libgff.tgz
##
#URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
#DOWNLOAD_NAME libff.tgz
diff --git a/cmake/Modules/FindTBB.cmake b/cmake/Modules/FindTBB.cmake
index c8b3eb5..b4c23da 100644
--- a/cmake/Modules/FindTBB.cmake
+++ b/cmake/Modules/FindTBB.cmake
@@ -184,7 +184,6 @@ if(NOT TBB_FOUND)
##################################
if(TBB_INCLUDE_DIRS)
- file(READ "${TBB_INCLUDE_DIRS}/tbb/tbb_stddef.h" _tbb_version_file)
string(REGEX REPLACE ".*#define TBB_VERSION_MAJOR ([0-9]+).*" "\\1"
TBB_VERSION_MAJOR "${_tbb_version_file}")
string(REGEX REPLACE ".*#define TBB_VERSION_MINOR ([0-9]+).*" "\\1"
diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh
index d32e131..1b5cbf2 100755
--- a/scripts/fetchPufferfish.sh
+++ b/scripts/fetchPufferfish.sh
@@ -10,18 +10,6 @@ CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
EXTERNAL_DIR=${CURR_DIR}/../external
INSTALL_DIR=${CURR_DIR}/../external/install
-if [ -d ${EXTERNAL_DIR}/pufferfish ] ; then
- rm -fr ${EXTERNAL_DIR}/pufferfish
-fi
-
-if [ -d ${INSTALL_DIR}/include/pufferfish ] ; then
- rm -fr ${INSTALL_DIR}/include/pufferfish
-fi
-
-if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then
- rm -fr ${INSTALL_DIR}/src/pufferfish
-fi
-
SVER=salmon-v1.6.0
#SVER=develop
#SVER=sketch-mode
@@ -29,31 +17,6 @@ SVER=salmon-v1.6.0
EXPECTED_SHA256=f71b3c08f254200fcdc2eb8fe3dcca8a8e9489e79ef5952a4958d8b9979831dc
mkdir -p ${EXTERNAL_DIR}
-curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip
-
-hashcheck=""
-if exists sha256sum; then
- hashcheck="sha256sum"
-elif exists shasum; then
- hashcheck="shasum -a256"
-else
- unset hashcheck
-fi
-
-if [ -z "${hashcheck-}" ]; then
- echo "Couldn't find shasum command; can't verify contents of downloaded pufferfish";
-else
- if [[ $SVER != develop ]]; then
- echo "${EXPECTED_SHA256} ${EXTERNAL_DIR}/pufferfish.zip" | ${hashcheck} -c - || { echo "pufferfish.zip did not match expected SHA1! Exiting."; exit 1; }
- else
- echo "not testing sha since pulling from develop"
- fi
-fi
-
-
-rm -fr ${EXTERNAL_DIR}/pufferfish
-unzip ${EXTERNAL_DIR}/pufferfish.zip -d ${EXTERNAL_DIR}
-mv ${EXTERNAL_DIR}/pufferfish-${SVER} ${EXTERNAL_DIR}/pufferfish
mkdir -p ${INSTALL_DIR}/include/pufferfish
|
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