From 3541914fb35a0d1598775fba21c6e0e70282431c Mon Sep 17 00:00:00 2001
From: Christopher Dunn <cdunn@pacificbiosciences.com>
Date: Mon, 21 May 2018 16:15:55 -0700
Subject: [PATCH] Install to /mnt/software, after building w/ dazzdb from there

---
 .gitignore      |  3 +++
 bamboo_build.sh | 57 ++++++++++++++++++++++++++++++++-----------------
 2 files changed, 40 insertions(+), 20 deletions(-)

diff --git a/.gitignore b/.gitignore
index b163ffd..7bf21ce 100644
--- a/.gitignore
+++ b/.gitignore
@@ -25,3 +25,6 @@
 
 # meson
 subprojects/dazz_db
+
+/DESTDIR/
+/build/
diff --git a/bamboo_build.sh b/bamboo_build.sh
index 6a953db..48f1f53 100755
--- a/bamboo_build.sh
+++ b/bamboo_build.sh
@@ -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