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#!/bin/bash
# Copyright [2015-2018] EMBL-European Bioinformatics Institute
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# Script for testing/installing various build configurations of Bio::DB::HTS
# $1 - clone command for Bio::DB::HTS from GitHub
# e.g. "git clone -b master https://github.com/Ensembl/Bio-DB-HTS.git"
# Set this to be an alternative clone command if required
# $2 - the test to be run, to match one of the options below
#
export PERL5LIB_ORIG=$PERL5LIB
#
# Tests the Build.PL with various options
#
if [ "$2" = "BUILD_SYSTEM_INSTALLED_HTSLIB" ]; then
echo Installs htslib, then runs Bio::DB::HTS Build process
git clone -b master --depth=1 https://github.com/samtools/htslib.git
cd htslib
sudo make install
cd ..
$1
cd Bio-DB-HTS
perl Build.PL
./Build
export PERL5LIB=$PERL5LIB:$(pwd -P)/lib:$(pwd -P)/blib/arch/auto/Bio/DB/HTS/:$(pwd -P)/blib/arch/auto/Bio/DB/HTS/Faidx
cd t
for f in $(ls *.t) ;
do
perl $f
done
echo "Completed $2"
export PERL5LIB=$PERL5LIB_ORIG
exit 0
fi
if [ "$2" = "BUILD_SYSTEM_INSTALL_ALL" ]; then
echo Installs htslib, then builds and installs Bio::DB::HTS
git clone -b master --depth=1 https://github.com/samtools/htslib.git
cd htslib
sudo make install
sudo ldconfig
cd ..
$1
cd Bio-DB-HTS
perl Build.PL
sudo ./Build install
cd t
for f in $(ls *.t) ;
do
perl $f
done
echo "Completed $2"
exit 0
fi
if [ "$2" = "BUILD_LOCAL_INSTALLED_HTSLIB" ]; then
echo Installs htslib and Bio::DB::HTS to a local dir
echo Specifies htslib dir using --prefix
git clone -b master --depth=1 https://github.com/samtools/htslib.git
cd htslib
make prefix=~/localsw install
export HTSLIB_DIR=
cd ..
$1
cd Bio-DB-HTS
perl Build.PL --prefix=~/localsw
./Build
export PERL5LIB=$PERL5LIB:$(pwd -P)/lib:$(pwd -P)/blib/arch/auto/Bio/DB/HTS/:$(pwd -P)/blib/arch/auto/Bio/DB/HTS/Faidx
cd t
for f in $(ls *.t) ;
do
perl $f
done
echo "Completed $2"
export PERL5LIB=$PERL5LIB_ORIG
exit 0
fi
if [ "$2" = "BUILD_HTSLIB_DIR_ENV" ]; then
echo Builds htslib, then runs Bio::DB::HTS Build process. Should run from this location.
echo Specifies htslib location with HTSLIB_DIR environment variable
git clone -b master --depth=1 https://github.com/samtools/htslib.git
cd htslib
make
export HTSLIB_DIR="$PWD"
echo $HTSLIB_DIR
cd ..
$1
cd Bio-DB-HTS
perl Build.PL
./Build
export PERL5LIB=$PERL5LIB:$(pwd -P)/lib:$(pwd -P)/blib/arch/auto/Bio/DB/HTS/:$(pwd -P)/blib/arch/auto/Bio/DB/HTS/Faidx
cd t
for f in $(ls *.t) ;
do
perl $f
done
echo "Completed $2"
export PERL5LIB=$PERL5LIB_ORIG
exit 0
fi
if [ "$2" = "BUILD_HTSLIB_DIR_FLAG" ]; then
echo Makes htslib, then runs Bio::DB::HTS Build process
echo Specifies htslib location with --htslib flag
git clone -b master --depth=1 https://github.com/samtools/htslib.git
cd htslib
make
export HTSLIB_DIR_FOR_FLAG="$PWD"
echo $HTSLIB_DIR_FOR_FLAG
cd ..
$1
cd Bio-DB-HTS
perl Build.PL --htslib=$HTSLIB_DIR_FOR_FLAG
./Build
export PERL5LIB=$PERL5LIB:$(pwd -P)/lib:$(pwd -P)/blib/arch/auto/Bio/DB/HTS/:$(pwd -P)/blib/arch/auto/Bio/DB/HTS/Faidx
cd t
for f in $(ls *.t) ;
do
perl $f
done
echo "Completed $2"
export PERL5LIB=$PERL5LIB_ORIG
exit 0
fi
#TODO Alien::HTSlib dependency resolver
#TODO pkg-config test
#Test the static option using the INSTALL_STATIC_FLAG option
#
#test the INSTALL.pl script with various options
#
if [ "$2" = "INSTALL_WITH_SYSTEM_HTSLIB" ]; then
echo INSTALL.pl with system install of htslib for running
git clone -b master --depth=1 https://github.com/samtools/htslib.git
cd htslib
sudo make install
sudo ldconfig
cd ..
$1
cd Bio-DB-HTS
perl INSTALL.pl
cd t
for f in $(ls *.t) ;
do
perl $f
done
echo "Completed $2"
exit 0
fi
if [ "$2" = "INSTALL_WITH_OTHER_HTSLIB" ]; then
echo INSTALL.pl, with a htslib installed elsewhere for running
export LD_LIBRARY_PATH_ORIG=$LD_LIBRARY_PATH
git clone -b master --depth=1 https://github.com/samtools/htslib.git htslib_run_location
cd htslib_run_location
make
cd ..
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$(pwd -P)/htslib_run_location
$1
cd Bio-DB-HTS
perl INSTALL.pl
cd t
for f in $(ls *.t) ;
do
perl $f
done
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH_ORIG
echo "Completed $2"
exit 0
fi
if [ "$2" = "INSTALL_PREFIX_PATH" ]; then
echo INSTALL.pl with prefix at end of line
$1
cd Bio-DB-HTS
perl INSTALL.pl ~/prefix_path_test
export PERL5LIB=$PERL5LIB:~/prefix_path_test/lib/perl5/x86_64-linux-gnu-thread-multi/:~/prefix_path_test/lib/perl5/x86_64-linux-gnu-thread-multi/auto
cd t
for f in $(ls *.t) ;
do
perl $f
done
echo "Completed $2"
export PERL5LIB=$PERL5LIB_ORIG
exit 0
fi
if [ "$2" = "INSTALL_PREFIX_FLAG" ]; then
echo INSTALL.pl with prefix at end of line
$1
cd Bio-DB-HTS
perl INSTALL.pl --prefix=~/prefix_flag_test
export PERL5LIB=$PERL5LIB:~/prefix_flag_test/lib/perl5/x86_64-linux-gnu-thread-multi/:~/prefix_flag_test/lib/perl5/x86_64-linux-gnu-thread-multi/auto
cd t
for f in $(ls *.t) ;
do
perl $f
done
echo "Completed $2"
export PERL5LIB=$PERL5LIB_ORIG
exit 0
fi
if [ "$2" = "INSTALL_STATIC_FLAG" ]; then
echo INSTALL.pl with static option as flag
$1
cd Bio-DB-HTS
perl INSTALL.pl --static
cd t
for f in $(ls *.t) ;
do
perl $f
done
echo "Completed $2"
exit 0
fi
if [ "$2" = "INSTALL_HTSLIB_VERSION" ]; then
echo INSTALL.pl built against a specific release of HTSlib
$1
cd Bio-DB-HTS
perl INSTALL.pl --htslib_version 1.3
export PERL5LIB=$PERL5LIB:$(pwd -P)/lib:$(pwd -P)/blib/arch/auto/Bio/DB/HTS/:$(pwd -P)/blib/arch/auto/Bio/DB/HTS/Faidx
cd t
for f in $(ls *.t) ;
do
perl $f
done
echo "Completed $2"
exit 0
fi
echo Build test option $2 not found
|
