Merge pull request PacificBiosciences#24 in SAT/daligner from feature…

…/TAG-2490-shared-is-fine-if-it-works to develop

* commit 'dc5b25bed0f5611744f779a47ac16550b7424246':
  DAZZ_DB artifacts changed
  Revert "Only build daligner using static libraries"

bamboo_build.sh

@@ -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

meson.build

@@ -44,11 +44,22 @@ daligner_deps = [daligner_m_dep, daligner_thread_dep, daligner_dazzdb_dep]
 # binaries #
 ############
 
-daligner_lib = static_library(
+# install library if
+# - either running as a proper project
+# - or using shared libraries
+daligner_lib_install = (not meson.is_subproject()) or (get_option('default_library') == 'shared')
+
+daligner_lib = library(
   'daligner',
   files([
     'align.c']),
-  install : (not meson.is_subproject()),
+  # use boost SONAME practice:
+  #   cause ld startup issues before
+  #   you even have the chance of running
+  #   into ABI issues.
+  soversion : meson.project_version(),
+  version : meson.project_version(),
+  install : daligner_lib_install,
   dependencies : daligner_deps,
   c_args : daligner_flags)