1 files changed, 60 insertions, 0 deletions
diff --git a/pkgs/by-name/sa/salmon/fetch-pufferfish.patch b/pkgs/by-name/sa/salmon/fetch-pufferfish.patch
new file mode 100644
index 000000000000..7010a1a69fac
--- /dev/null
+++ b/pkgs/by-name/sa/salmon/fetch-pufferfish.patch
@@ -0,0 +1,60 @@
+diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh
+index bf2574e0..42582806 100755
+--- a/scripts/fetchPufferfish.sh
++++ b/scripts/fetchPufferfish.sh
+@@ -11,10 +11,6 @@ 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
+@@ -23,42 +19,10 @@ if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then
+     rm -fr ${INSTALL_DIR}/src/pufferfish
+ fi
+ 
+-SVER=salmon-v1.10.2
+-#SVER=develop
+-#SVER=sketch-mode
+-
+-EXPECTED_SHA256=f225b74833f71dcf767a565345224357fb091f90ce79717abc836814d9ccd101
+-
+-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 && $SVER != onetbb ]]; then
+-        echo "${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
++# This is needed later when pufferfish is compiled for Salmon
++cp -r ${pufferFishSrc} ${EXTERNAL_DIR}/pufferfish
+ 
+ cp ${EXTERNAL_DIR}/pufferfish/include/ProgOpts.hpp ${INSTALL_DIR}/include/pufferfish
+ cp ${EXTERNAL_DIR}/pufferfish/include/BooPHF.hpp ${INSTALL_DIR}/include/pufferfish