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We will switch this build to Meson soon, but that is not the
purpose of *this* change. One thing at a time.
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Christopher Dunn committed May 21, 2018
1 parent fcc66a7 commit dc5b25b
Showing 1 changed file with 13 additions and 10 deletions.
23 changes: 13 additions & 10 deletions bamboo_build.sh
Original file line number Diff line number Diff line change
@@ -1,30 +1,33 @@
#!/bin/bash -ex
#!/bin/bash -e
type module >& /dev/null || source /mnt/software/Modules/current/init/bash

set -vex
module load gcc/6.4.0
module load git/2.8.3
module load ccache

set -vex

NEXUS_BASEURL=http://ossnexus.pacificbiosciences.com/repository
NEXUS_URL=$NEXUS_BASEURL/unsupported/gcc-6.4.0

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/*.a DAZZ_DB/
cp prebuilt/DAZZ_DB/include/*.h DAZZ_DB/
cp prebuilt/DAZZ_DB/lib/lib* DAZZ_DB/
cp prebuilt/DAZZ_DB/include/dazzdb/*.h DAZZ_DB/

make -C DALIGNER clean
make -C DALIGNER LIBDIRS=$PWD/prebuilt/DAZZ_DB/lib -j
make -C DALIGNER PREFIX=$PWD/build install
make clean
make LIBDIRS=$PWD/prebuilt/DAZZ_DB/lib -j
make PREFIX=$PWD/build install

make -f /dept/secondary/siv/testdata/hgap/synth5k/LA4Falcon/makefile clean
PATH=.:${PATH} make -C DALIGNER -f /dept/secondary/siv/testdata/hgap/synth5k/LA4Falcon/makefile
PATH=.:${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
cd build
tar zcf DALIGNER-SNAPSHOT.tgz bin
curl -v -n --upload-file DALIGNER-SNAPSHOT.tgz $NEXUS_URL/DALIGNER-SNAPSHOT.tgz
fi

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