diff options
| author | Jason W. Bacon <jwb@FreeBSD.org> | 2025-07-27 16:04:26 -0500 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2025-07-27 16:04:26 -0500 |
| commit | ace12788b0dbb0a71c23a618c534595c96b44205 (patch) | |
| tree | 868e324a5283d7c0dc93e8ec33d1cf37e9e59477 /biology/salmon/files/patch-scripts_fetchPufferfish.sh | |
| parent | multimedia/openh264: security update to v2.6.0 (diff) | |
biology/salmon: Update to tag 1.10.3
Fix build under clang19:
Patch out deprecated atomic template copy
Unbundle eigen and libdivide
https://github.com/COMBINE-lab/salmon/issues/988
Upstream updates to improve ARM support
Changes: https://github.com/COMBINE-lab/salmon/commits/master/
Reported by: pkg-fallout
Diffstat (limited to 'biology/salmon/files/patch-scripts_fetchPufferfish.sh')
| -rw-r--r-- | biology/salmon/files/patch-scripts_fetchPufferfish.sh | 27 |
1 files changed, 17 insertions, 10 deletions
diff --git a/biology/salmon/files/patch-scripts_fetchPufferfish.sh b/biology/salmon/files/patch-scripts_fetchPufferfish.sh index 566493a5e7ee..a1885fd1ff61 100644 --- a/biology/salmon/files/patch-scripts_fetchPufferfish.sh +++ b/biology/salmon/files/patch-scripts_fetchPufferfish.sh @@ -1,15 +1,13 @@ ---- scripts/fetchPufferfish.sh.orig 2023-07-21 13:59:29 UTC +--- scripts/fetchPufferfish.sh.orig 2025-07-26 17:38:39 UTC +++ scripts/fetchPufferfish.sh -@@ -11,52 +11,12 @@ CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && p +@@ -11,53 +11,6 @@ INSTALL_DIR=${CURR_DIR}/../external/install EXTERNAL_DIR=${CURR_DIR}/../external INSTALL_DIR=${CURR_DIR}/../external/install -if [ -d ${EXTERNAL_DIR}/pufferfish ] ; then - rm -fr ${EXTERNAL_DIR}/pufferfish -fi -+# Pufferfish is downloaded using GH_TUPLE in the FreeBSD port, so remove -+# code here that downloads and unpacks - +- -if [ -d ${INSTALL_DIR}/include/pufferfish ] ; then - rm -fr ${INSTALL_DIR}/include/pufferfish -fi @@ -18,11 +16,11 @@ - rm -fr ${INSTALL_DIR}/src/pufferfish -fi - - SVER=salmon-v1.10.2 - #SVER=develop - #SVER=sketch-mode +-SVER=salmon-v1.10.3 +-#SVER=develop +-#SVER=sketch-mode - --EXPECTED_SHA256=f225b74833f71dcf767a565345224357fb091f90ce79717abc836814d9ccd101 +-EXPECTED_SHA256=52b6699de0d33814b73edb3455175568c2330d8014be017dce7b564e54134860 - -mkdir -p ${EXTERNAL_DIR} -curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip @@ -52,6 +50,15 @@ -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 + cp ${EXTERNAL_DIR}/pufferfish/include/ProgOpts.hpp ${INSTALL_DIR}/include/pufferfish +@@ -90,7 +43,6 @@ cp ${EXTERNAL_DIR}/pufferfish/include/BinWriter.hpp ${ + 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 + # this is now automatically tracked and inherited via twopaco (on which libpuffer depends) + # cp -r ${EXTERNAL_DIR}/pufferfish/include/compact_vector ${INSTALL_DIR}/include/pufferfish |