pkgs/by-name/sa/salmon/fetch-pufferfish.patch

   1 diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh
   2 index 95e30053..8866767c 100755
   3 --- a/scripts/fetchPufferfish.sh
   4 +++ b/scripts/fetchPufferfish.sh
   5 @@ -11,10 +11,6 @@ CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
   6  EXTERNAL_DIR=${CURR_DIR}/../external
   7  INSTALL_DIR=${CURR_DIR}/../external/install
   8
   9 -if [ -d ${EXTERNAL_DIR}/pufferfish ] ; then
  10 -    rm -fr ${EXTERNAL_DIR}/pufferfish
  11 -fi
  12 -
  13  if [ -d ${INSTALL_DIR}/include/pufferfish ] ; then
  14      rm -fr ${INSTALL_DIR}/include/pufferfish
  15  fi
  16 @@ -23,42 +19,10 @@ if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then
  17      rm -fr ${INSTALL_DIR}/src/pufferfish
  18  fi
  19
  20 -SVER=salmon-v1.10.3
  21 -#SVER=develop
  22 -#SVER=sketch-mode
  23 -
  24 -EXPECTED_SHA256=52b6699de0d33814b73edb3455175568c2330d8014be017dce7b564e54134860
  25 -
  26 -mkdir -p ${EXTERNAL_DIR}
  27 -curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip
  28 -
  29 -hashcheck=""
  30 -if exists sha256sum; then
  31 -       hashcheck="sha256sum"
  32 -elif exists shasum; then
  33 -       hashcheck="shasum -a256"
  34 -else
  35 -       unset hashcheck
  36 -fi
  37 -
  38 -
  39 -if [ -z "${hashcheck-}" ]; then
  40 -    echo "Couldn't find shasum command; can't verify contents of downloaded pufferfish";
  41 -else
  42 -
  43 -    if [[ $SVER != develop && $SVER != onetbb ]]; then
  44 -        echo "${EXPECTED_SHA256}  ${EXTERNAL_DIR}/pufferfish.zip" | ${hashcheck} -c - || { echo "pufferfish.zip did not match expected SHA1! Exiting."; exit 1; }
  45 -    else
  46 -        echo "not testing sha since pulling from develop"
  47 -    fi
  48 -fi
  49 -
  50 -
  51 -rm -fr ${EXTERNAL_DIR}/pufferfish
  52 -unzip ${EXTERNAL_DIR}/pufferfish.zip -d ${EXTERNAL_DIR}
  53 -mv ${EXTERNAL_DIR}/pufferfish-${SVER} ${EXTERNAL_DIR}/pufferfish
  54
  55  mkdir -p ${INSTALL_DIR}/include/pufferfish
  56 +# This is needed later when pufferfish is compiled for Salmon
  57 +cp -r ${pufferFishSrc} ${EXTERNAL_DIR}/pufferfish
  58
  59  cp ${EXTERNAL_DIR}/pufferfish/include/ProgOpts.hpp ${INSTALL_DIR}/include/pufferfish
  60  cp ${EXTERNAL_DIR}/pufferfish/include/BooPHF.hpp ${INSTALL_DIR}/include/pufferfish