forked from PacificBiosciences/DALIGNER
-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Install to /mnt/software, after building w/ dazzdb from there
- Loading branch information
Christopher Dunn
committed
May 21, 2018
1 parent
3399c92
commit 3541914
Showing
2 changed files
with
40 additions
and
20 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -25,3 +25,6 @@ | |
|
||
# meson | ||
subprojects/dazz_db | ||
|
||
/DESTDIR/ | ||
/build/ |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,33 +1,50 @@ | ||
#!/bin/bash -e | ||
type module >& /dev/null || source /mnt/software/Modules/current/init/bash | ||
|
||
module load gcc/6.4.0 | ||
module load git/2.8.3 | ||
module load gcc | ||
module load git | ||
module load meson | ||
module load ninja | ||
module load ccache | ||
|
||
set -vex | ||
|
||
NEXUS_BASEURL=http://ossnexus.pacificbiosciences.com/repository | ||
NEXUS_URL=$NEXUS_BASEURL/unsupported/gcc-6.4.0 | ||
export CCACHE_COMPILERCHECK='%compiler% -dumpversion' | ||
|
||
rm -rf prebuilt build | ||
mkdir -p prebuilt/DAZZ_DB build/bin | ||
curl -s -L $NEXUS_URL/DAZZ_DB-SNAPSHOT.tgz|tar zxf - -C prebuilt/DAZZ_DB | ||
mkdir -p DAZZ_DB | ||
cp prebuilt/DAZZ_DB/lib/lib* DAZZ_DB/ | ||
cp prebuilt/DAZZ_DB/include/dazzdb/*.h DAZZ_DB/ | ||
case "${bamboo_planRepository_branchName}" in | ||
develop|master) | ||
module load dazzdb/${bamboo_planRepository_branchName} | ||
export PREFIX_ARG="/mnt/software/d/dazzdb/${bamboo_planRepository_branchName}" | ||
export BUILD_NUMBER="${bamboo_globalBuildNumber:-0}" | ||
;; | ||
*) | ||
module load dazzdb/develop | ||
export PREFIX_ARG=/PREFIX | ||
export BUILD_NUMBER="0" | ||
;; | ||
esac | ||
|
||
make clean | ||
make LIBDIRS=$PWD/prebuilt/DAZZ_DB/lib -j | ||
make PREFIX=$PWD/build install | ||
# rm -rf ./build | ||
meson --buildtype=release --strip --libdir=lib --prefix="${PREFIX_ARG}" -Dtests=false --wrap-mode nofallback ./build . | ||
|
||
TERM='dumb' ninja -C ./build -v | ||
|
||
DESTDIR="$(pwd)/DESTDIR" | ||
rm -rf "${DESTDIR}" | ||
TERM='dumb' DESTDIR="${DESTDIR}" ninja -C ./build -v install | ||
|
||
make -f /dept/secondary/siv/testdata/hgap/synth5k/LA4Falcon/makefile clean | ||
PATH=.:${PATH} make -f /dept/secondary/siv/testdata/hgap/synth5k/LA4Falcon/makefile | ||
PATH="${DESTDIR}${PREFIX_ARG}/bin":${PATH} LD_LIBRARY_PATH="${DESTDIR}${PREFIX_ARG}/lib":${LD_LIBRARY_PATH} make -f /dept/secondary/siv/testdata/hgap/synth5k/LA4Falcon/makefile | ||
make -f /dept/secondary/siv/testdata/hgap/synth5k/LA4Falcon/makefile clean | ||
|
||
cd build | ||
tar vzcf DALIGNER-SNAPSHOT.tgz bin | ||
|
||
if [[ $bamboo_planRepository_branchName == "develop" ]]; then | ||
curl -v -n --upload-file DALIGNER-SNAPSHOT.tgz $NEXUS_URL/DALIGNER-SNAPSHOT.tgz | ||
fi | ||
rm -rf "${DESTDIR}" | ||
|
||
case "${bamboo_planRepository_branchName}" in | ||
develop|master) | ||
DESTDIR= | ||
TERM='dumb' DESTDIR="${DESTDIR}" ninja -C ./build -v install | ||
chmod -R a+rwx "${DESTDIR}${PREFIX_ARG}"/* | ||
module load daligner/${bamboo_planRepository_branchName} | ||
ldd -r $(which DBshow) | ||
;; | ||
esac |