pyrox.dev
1diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh
2index 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