New upstream version 0.3+git20180411.c14c422+ds

  src/filterm4.py 'code'

[pbdagcon_wf.sh]:

  src/cpp/pbdagcon_wf.sh 'code'

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#!/bin/bash

set -e

NEXUS_BASEURL=http://ossnexus.pacificbiosciences.com/repository

#NEXUS_URL=$NEXUS_BASEURL/unsupported/gcc-4.9.2

if [ ! -e .distfiles/gtest/release-1.7.0.tar.gz ]; then

  mkdir -p .distfiles/gtest

  curl -sL $NEXUS_BASEURL/unsupported/distfiles/googletest/release-1.7.0.tar.gz \

    -o .distfiles/gtest/release-1.7.0.tar.gz

fi

tar zxf .distfiles/gtest/release-1.7.0.tar.gz -C repos/

ln -sfn googletest-release-1.7.0 repos/gtest

rm -rf deployment

mkdir -p deployment

/bin/ls -t tarballs/pbbam-*.tgz        | head -1 | xargs -r -n 1 cat | tar zxv --strip-components 3 -C deployment

/bin/ls -t tarballs/blasr_libcpp-*.tgz | head -1 | xargs -r -n 1 cat | tar zxv --strip-components 3 -C deployment

/bin/ls -t tarballs/blasr-*.tgz        | head -1 | xargs -r -n 1 cat | tar zxv --strip-components 2 -C deployment

DEPLOYMENT=$PWD/deployment

export PATH=$PWD/deployment/bin:$PATH

export LD_LIBRARY_PATH=$PWD/deployment/lib:$LD_LIBRARY_PATH

type module >& /dev/null || . /mnt/software/Modules/current/init/bash

module load git

module load gcc

module load ccache

if [[ $USER == bamboo ]]; then

  export CCACHE_DIR=/mnt/secondary/Share/tmp/bamboo.mobs.ccachedir

fi

module load boost

if [[ $BOOST_ROOT =~ /include ]]; then

  set -x

  BOOST_ROOT=$(dirname $BOOST_ROOT)

  set +x

fi

module load htslib

module load hdf5-tools

module load zlib

DAZZDB=$PWD/repos/dazzdb

DALIGNER=$PWD/repos/daligner

cd repos/pbdagcon

export CCACHE_BASEDIR=$PWD

rm -rf build

set -x

mkdir -p build

    BOOST_INCLUDE=$BOOST_ROOT/include \

LIBPBDATA_INCLUDE=$DEPLOYMENT/include/pbdata \

    LIBPBDATA_LIB=$DEPLOYMENT/lib \

 LIBBLASR_INCLUDE=$DEPLOYMENT/include/alignment \

     LIBBLASR_LIB=$DEPLOYMENT/lib \

LIBPBIHDF_INCLUDE=$DEPLOYMENT/include/hdf \

    LIBPBIHDF_LIB=$DEPLOYMENT/lib \

    PBBAM_INCLUDE=$DEPLOYMENT/include \

        PBBAM_LIB=$DEPLOYMENT/lib \

    HTSLIB_CFLAGS=$(pkg-config --cflags htslib) \

      HTSLIB_LIBS=$(pkg-config --libs htslib) \

     HDF5_INCLUDE=$(pkg-config --cflags-only-I hdf5|awk '{print $1}'|sed -e 's/^-I//') \

         HDF5_LIB=$(pkg-config --libs-only-L hdf5|awk '{print $1}'|sed -e 's/^-L//') \

     DALIGNER_SRC=$DALIGNER \

      DAZZ_DB_SRC=$DAZZDB \

        GTEST_SRC=$PWD/../gtest/src \

    GTEST_INCLUDE=$PWD/../gtest/include \

    ZLIB_LIBFLAGS="$(pkg-config --libs zlib)" \

./configure.py --build-dir=$PWD/build

sed -i -e 's/-lpbihdf/-llibcpp/;s/-lblasr//;s/-lpbdata//' build/defines.mk

make -C build

cp -a build/src/cpp/pbdagcon $DEPLOYMENT/bin/

cp -a build/src/cpp/dazcon   $DEPLOYMENT/bin/

cd ../..

myVERSION=`pbdagcon --version|awk '/version/{print $3}'`

#rm -rf tarballs && mkdir -p tarballs

cd deployment

tar zcf ../tarballs/pbdagcon-${myVERSION}.tgz bin/pbdagcon bin/dazcon

#!/bin/bash

export PATH=$PWD/deployment/bin:$PATH

export LD_LIBRARY_PATH=$PWD/deployment/lib:$LD_LIBRARY_PATH

type module >& /dev/null \

|| . /mnt/software/Modules/current/init/bash

module load gcc

module load htslib

module load hdf5-tools

module load zlib

make -C repos/pbdagcon/build check

chmod +w -R repos/pbdagcon

            'LIBPBIHDF_INCLUDE', 'LIBPBIHDF_LIB', 'LIBPBIHDF_LIBFLAGS',

            'HDF5_INCLUDE', 'HDF5_LIB', 'HDF5_LIBFLAGS',

            'PBBAM_INCLUDE', 'PBBAM_LIB', 'PBBAM_LIBFLAGS',

            'HTSLIB_INCLUDE', 'HTSLIB_LIB', 'HTSLIB_LIBFLAGS',

            'HTSLIB_CFLAGS', 'HTSLIB_LIBS',

            'BOOST_INCLUDE', 'PTHREAD_LIBFLAGS',

            'ZLIB_LIB', 'ZLIB_LIBFLAGS',

            'GCC_LIB',

    pbbam_defaults = {

        'LIBPBIHDF_LIBFLAGS': '-lpbihdf',

        'PBBAM_LIBFLAGS': '-lpbbam',

        'HTSLIB_LIBFLAGS': '-lhts',

        'HTSLIB_LIBS': '-lhts',

        'HDF5_LIBFLAGS': '-lhdf5_cpp -lhdf5',

        'ZLIB_LIBFLAGS': '-lz',

        'PTHREAD_LIBFLAGS': '-lpthread',

// daligner structures.

Target::Target(): needsFree_(false) { }

Target::Target(HITS_DB& db, int tspace, int small) :

Target::Target(DAZZ_DB& db, int tspace, int small) :

    db_(db),

    tspace_(tspace),

    small_(small),