diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh index 80e4b42ae..fd20f5879 100755 --- a/scripts/fetchPufferfish.sh +++ b/scripts/fetchPufferfish.sh @@ -4,6 +4,7 @@ set -eu -o pipefail exists() { command -v "$1" >/dev/null 2>&1 + } CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd ) @@ -22,11 +23,11 @@ if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then rm -fr ${INSTALL_DIR}/src/pufferfish fi -#SVER=salmon-v1.6.0 -SVER=develop +SVER=salmon-v1.7.0 +#SVER=develop #SVER=sketch-mode -EXPECTED_SHA256=f71b3c08f254200fcdc2eb8fe3dcca8a8e9489e79ef5952a4958d8b9979831dc +EXPECTED_SHA256=5894fabbf6829a3d4a627135edc8326e931eb07fc792bfff3a0714e8fee8bb8b mkdir -p ${EXTERNAL_DIR} curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip @@ -40,9 +41,11 @@ else unset hashcheck fi + if [ -z "${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 @@ -83,8 +86,10 @@ cp ${EXTERNAL_DIR}/pufferfish/include/MemChainer.hpp ${INSTALL_DIR}/include/puff cp ${EXTERNAL_DIR}/pufferfish/include/CommonTypes.hpp ${INSTALL_DIR}/include/pufferfish cp ${EXTERNAL_DIR}/pufferfish/include/SAMWriter.hpp ${INSTALL_DIR}/include/pufferfish cp ${EXTERNAL_DIR}/pufferfish/include/PufferfishConfig.hpp ${INSTALL_DIR}/include/pufferfish + cp ${EXTERNAL_DIR}/pufferfish/include/BulkChunk.hpp ${INSTALL_DIR}/include/pufferfish cp ${EXTERNAL_DIR}/pufferfish/include/BinWriter.hpp ${INSTALL_DIR}/include/pufferfish + cp -r ${EXTERNAL_DIR}/pufferfish/include/libdivide ${INSTALL_DIR}/include/pufferfish cp -r ${EXTERNAL_DIR}/pufferfish/include/ksw2pp ${INSTALL_DIR}/include/pufferfish cp -r ${EXTERNAL_DIR}/pufferfish/include/compact_vector ${INSTALL_DIR}/include/pufferfish @@ -116,6 +121,7 @@ cp ${EXTERNAL_DIR}/pufferfish/src/rank9b.cpp ${INSTALL_DIR}/src/pufferfish #cp -r ${EXTERNAL_DIR}/RapMap/include/*.hpp ${INSTALL_DIR}/include/rapmap #cp -r ${EXTERNAL_DIR}/RapMap/include/sparsepp ${INSTALL_DIR}/include/rapmap #cp -r ${EXTERNAL_DIR}/RapMap/include/digestpp ${INSTALL_DIR}/include/rapmap + #cp -r ${EXTERNAL_DIR}/RapMap/include/itlib ${INSTALL_DIR}/include/rapmap #cp -r ${EXTERNAL_DIR}/RapMap/include/metro ${INSTALL_DIR}/include/rapmap #cp -r ${EXTERNAL_DIR}/RapMap/include/ksw2pp ${INSTALL_DIR}/include/rapmap @@ -127,4 +133,5 @@ cp ${EXTERNAL_DIR}/pufferfish/src/rank9b.cpp ${INSTALL_DIR}/src/pufferfish #rm ${INSTALL_DIR}/include/rapmap/FastxParser.hpp #rm ${INSTALL_DIR}/include/rapmap/concurrentqueue.h #rm ${INSTALL_DIR}/include/rapmap/FastxParserThreadUtils.hpp + #rm ${INSTALL_DIR}/src/rapmap/FastxParser.cpp