60 lines
1.9 KiB
Diff
60 lines
1.9 KiB
Diff
diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh
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index bf2574e0..42582806 100755
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--- a/scripts/fetchPufferfish.sh
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+++ b/scripts/fetchPufferfish.sh
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@@ -11,10 +11,6 @@ CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
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EXTERNAL_DIR=${CURR_DIR}/../external
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INSTALL_DIR=${CURR_DIR}/../external/install
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-if [ -d ${EXTERNAL_DIR}/pufferfish ] ; then
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- rm -fr ${EXTERNAL_DIR}/pufferfish
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-fi
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-
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if [ -d ${INSTALL_DIR}/include/pufferfish ] ; then
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rm -fr ${INSTALL_DIR}/include/pufferfish
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fi
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@@ -23,42 +19,10 @@ if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then
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rm -fr ${INSTALL_DIR}/src/pufferfish
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fi
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-SVER=salmon-v1.10.2
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-#SVER=develop
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-#SVER=sketch-mode
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-
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-EXPECTED_SHA256=f225b74833f71dcf767a565345224357fb091f90ce79717abc836814d9ccd101
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-
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-mkdir -p ${EXTERNAL_DIR}
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-curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip
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-
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-hashcheck=""
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-if exists sha256sum; then
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- hashcheck="sha256sum"
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-elif exists shasum; then
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- hashcheck="shasum -a256"
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-else
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- unset hashcheck
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-fi
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-
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-
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-if [ -z "${hashcheck-}" ]; then
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- echo "Couldn't find shasum command; can't verify contents of downloaded pufferfish";
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-else
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-
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- if [[ $SVER != develop && $SVER != onetbb ]]; then
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- echo "${EXPECTED_SHA256} ${EXTERNAL_DIR}/pufferfish.zip" | ${hashcheck} -c - || { echo "pufferfish.zip did not match expected SHA1! Exiting."; exit 1; }
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- else
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- echo "not testing sha since pulling from develop"
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- fi
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-fi
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-
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-
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-rm -fr ${EXTERNAL_DIR}/pufferfish
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-unzip ${EXTERNAL_DIR}/pufferfish.zip -d ${EXTERNAL_DIR}
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-mv ${EXTERNAL_DIR}/pufferfish-${SVER} ${EXTERNAL_DIR}/pufferfish
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mkdir -p ${INSTALL_DIR}/include/pufferfish
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+# This is needed later when pufferfish is compiled for Salmon
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+cp -r ${pufferFishSrc} ${EXTERNAL_DIR}/pufferfish
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cp ${EXTERNAL_DIR}/pufferfish/include/ProgOpts.hpp ${INSTALL_DIR}/include/pufferfish
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cp ${EXTERNAL_DIR}/pufferfish/include/BooPHF.hpp ${INSTALL_DIR}/include/pufferfish
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