Merge pull request #44 from ICGC-TCGA-PanCancer/dev

v1.1.1

MANIFEST

@@ -1,5 +1,6 @@
 bin/bam_stats.pl
 bin/bam_to_sra_sub.pl
+bin/build_biobambam_relocatable.sh
 bin/bwa_aln.pl
 bin/bwa_mem.pl
 bin/cpanm

MYMETA.json

@@ -49,10 +49,11 @@
             "Sub::Exporter::Progressive" : "0.001011",
             "Term::UI" : "0.42",
             "Test::Fatal" : "0.013",
-            "Try::Tiny" : "0.19"
+            "Try::Tiny" : "0.19",
+            "XML::Simple" : "2.2"
          }
       }
    },
    "release_status" : "stable",
-   "version" : "v1.1.0"
+   "version" : "v1.1.1"
 }

MYMETA.yml

@@ -36,4 +36,5 @@ requires:
   Term::UI: 0.42
   Test::Fatal: 0.013
   Try::Tiny: 0.19
-version: v1.1.0
+  XML::Simple: 2.2
+version: v1.1.1

Makefile.PL

@@ -55,6 +55,7 @@ WriteMakefile(
                      'Pod::Coverage' => 0.23,
                      'Term::UI' => 0.42, # currently in core but scheduled for removal 5.17, no alternative recommended
                      'Sub::Exporter::Progressive' => 0.001011,
+                     'XML::Simple' => 2.20,
                    }
 );
 

bin/build_biobambam_relocatable.sh

@@ -0,0 +1,124 @@
+#! /bin/bash
+LIBMAUSVERSION=0.0.130-release-20140618101704
+BIOBAMBAMVERSION=0.0.148-release-20140618101902
+SNAPPYVERSION=1.1.1
+IOLIBVERSION=1.13.7
+CHRPATHVERSION=0.16
+BUILDDIR=${PWD}
+INSTALLDIR=${BUILDDIR}/install-dir
+TOOLSDIR=${BUILDDIR}/tools-dir
+PAR=`cat /proc/cpuinfo | egrep "^processor" | wc -l`
+
+# get chrpath
+if [ ! -f chrpath-${CHRPATHVERSION}.tar.gz ] ; then
+	wget -O - "https://alioth.debian.org/frs/download.php/file/3979/chrpath-${CHRPATHVERSION}.tar.gz" > chrpath-${CHRPATHVERSION}.tar.gz
+fi
+
+# get iolib
+if [ ! -f io_lib-${IOLIBVERSION}.tar.gz ] ; then
+	wget -O - "http://downloads.sourceforge.net/project/staden/io_lib/${IOLIBVERSION}/io_lib-${IOLIBVERSION}.tar.gz?&use_mirror=kent" \
+		> io_lib-${IOLIBVERSION}.tar.gz
+fi
+
+# get snappy
+if [ ! -f snappy-${SNAPPYVERSION}.tar.gz ] ; then
+	wget -O - https://snappy.googlecode.com/files/snappy-${SNAPPYVERSION}.tar.gz > snappy-${SNAPPYVERSION}.tar.gz
+fi
+
+# get libmaus
+if [ ! -f libmaus-${LIBMAUSVERSION}.tar.gz ] ; then
+	wget -O - https://github.com/gt1/libmaus/archive/${LIBMAUSVERSION}.tar.gz > libmaus-${LIBMAUSVERSION}.tar.gz
+fi
+
+# get biobambam
+if [ ! -f biobambam-${BIOBAMBAMVERSION}.tar.gz ] ; then
+	wget -O - https://github.com/gt1/biobambam/archive/${BIOBAMBAMVERSION}.tar.gz > biobambam-${BIOBAMBAMVERSION}.tar.gz
+fi
+
+tar xzvf chrpath-${CHRPATHVERSION}.tar.gz
+mv chrpath-${CHRPATHVERSION} chrpath-${CHRPATHVERSION}-src
+mkdir -p chrpath-${CHRPATHVERSION}-build
+cd chrpath-${CHRPATHVERSION}-build
+${BUILDDIR}/chrpath-${CHRPATHVERSION}-src/configure --prefix=${TOOLSDIR}
+make -j${PAR}
+make -j${PAR} install
+cd ..
+rm -fR chrpath-${CHRPATHVERSION}-src chrpath-${CHRPATHVERSION}-build
+
+rm -fR ${INSTALLDIR}
+mkdir -p ${INSTALLDIR}
+
+# build iolib
+tar xzvf io_lib-${IOLIBVERSION}.tar.gz
+mv io_lib-${IOLIBVERSION} io_lib-${IOLIBVERSION}-src
+mkdir -p io_lib-${IOLIBVERSION}-build
+cd io_lib-${IOLIBVERSION}-build
+LDFLAGS="-Wl,-rpath=XORIGIN/../lib" ${BUILDDIR}/io_lib-${IOLIBVERSION}-src/configure --prefix=${INSTALLDIR}
+make -j${PAR}
+make -j${PAR} install
+cd ..
+rm -fR io_lib-${IOLIBVERSION}-src io_lib-${IOLIBVERSION}-build
+
+# build snappy
+tar xzvf snappy-${SNAPPYVERSION}.tar.gz
+mv snappy-${SNAPPYVERSION} snappy-${SNAPPYVERSION}-src
+mkdir -p snappy-${SNAPPYVERSION}-build
+cd snappy-${SNAPPYVERSION}-build
+LDFLAGS="-Wl,-rpath=XORIGIN/../lib" ${BUILDDIR}/snappy-${SNAPPYVERSION}-src/configure --prefix=${INSTALLDIR}
+make -j${PAR}
+make -j${PAR} install
+cd ..
+rm -fR snappy-${SNAPPYVERSION}-src snappy-${SNAPPYVERSION}-build
+
+# build libmaus
+tar xzvf libmaus-${LIBMAUSVERSION}.tar.gz
+mv libmaus-${LIBMAUSVERSION} libmaus-${LIBMAUSVERSION}-src
+mkdir -p libmaus-${LIBMAUSVERSION}-build
+cd libmaus-${LIBMAUSVERSION}-build
+LDFLAGS="-Wl,-rpath=XORIGIN/../lib" ${BUILDDIR}/libmaus-${LIBMAUSVERSION}-src/configure --prefix=${INSTALLDIR} \
+	--with-snappy=${INSTALLDIR} \
+	--with-io_lib=${INSTALLDIR}
+make -j${PAR}
+make -j${PAR} install
+cd ..
+rm -fR libmaus-${LIBMAUSVERSION}-src libmaus-${LIBMAUSVERSION}-build
+
+# build biobambam
+tar xzvf biobambam-${BIOBAMBAMVERSION}.tar.gz
+mv biobambam-${BIOBAMBAMVERSION} biobambam-${BIOBAMBAMVERSION}-src
+mkdir -p biobambam-${BIOBAMBAMVERSION}-build
+cd biobambam-${BIOBAMBAMVERSION}-build
+LDFLAGS="-Wl,-rpath=XORIGIN/../lib" ${BUILDDIR}/biobambam-${BIOBAMBAMVERSION}-src/configure --prefix=${INSTALLDIR} \
+	--with-libmaus=${INSTALLDIR}
+make -j${PAR}
+make -j${PAR} install
+cd ..
+rm -fR biobambam-${BIOBAMBAMVERSION}-src biobambam-${BIOBAMBAMVERSION}-build
+
+for i in `find ${INSTALLDIR} -name \*.so\*` ; do
+	ORIG=`objdump -x ${i} | grep RPATH | awk '{print $2}'`
+	MOD=`echo "$ORIG" | sed "s/XORIGIN/\\$ORIGIN/"`
+	${TOOLSDIR}/bin/chrpath -r "${MOD}" ${i}
+done
+
+for i in ${INSTALLDIR}/bin/* ; do
+	if [ ! -z `LANG=C file ${i} | egrep "ELF.*executable" | awk '{print $1}' | perl -p -e "s/://"` ] ; then
+		ORIG=`objdump -x ${i} | grep RPATH | awk '{print $2}'`
+		MOD=`echo "$ORIG" | sed "s/XORIGIN/\\$ORIGIN/"`
+		${TOOLSDIR}/bin/chrpath -r "${MOD}" ${i}
+	fi
+done
+
+#mv ${INSTALLDIR} biobambam-${BIOBAMBAMVERSION}
+#tar czvf biobambam-${BIOBAMBAMVERSION}-`uname -p`-`uname -s`.tar.gz biobambam-${BIOBAMBAMVERSION}
+#rm -fR biobambam-${BIOBAMBAMVERSION}
+
+rm -fR ${TOOLSDIR}
+
+# my additions
+mv ${INSTALLDIR} biobambam
+rm -f chrpath-${CHRPATHVERSION}.tar.gz
+rm -f io_lib-${IOLIBVERSION}.tar.gz
+rm -f snappy-${SNAPPYVERSION}.tar.gz
+rm -f libmaus-${LIBMAUSVERSION}.tar.gz
+rm -f biobambam-${BIOBAMBAMVERSION}.tar.gz

lib/PCAP.pm

@@ -24,7 +24,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '1.1.0';
+our $VERSION = '1.1.1';
 our @EXPORT = qw($VERSION);
 
 const my $LICENSE =>
@@ -46,7 +46,8 @@ const my %UPGRADE_PATH => ( '0.1.0'  => 'biobambam,samtools,bwa',
                             '1.0.2'  => 'biobambam,bwa',
                             '1.0.3'  => 'biobambam',
                             '1.0.4'  => 'biobambam',
-                            '1.1.0'  => '',
+                            '1.1.0'  => 'biobambam',
+                            '1.1.1'  => '',
                           );
 
 sub license {

setup.sh

@@ -1,10 +1,6 @@
 #!/bin/bash
 
 SOURCE_BWA="https://github.com/lh3/bwa/archive/0.7.8.tar.gz"
-SOURCE_SNAPPY="https://snappy.googlecode.com/files/snappy-1.1.1.tar.gz"
-SOURCE_IOLIB="http://sourceforge.net/projects/staden/files/io_lib/1.13.7/io_lib-1.13.7.tar.gz/download"
-SOURCE_LIBMAUS="https://github.com/gt1/libmaus/archive/0.0.127-release-20140602112423.tar.gz"
-SOURCE_BIOBAMBAM="https://github.com/gt1/biobambam/archive/0.0.147-release-20140602113434.tar.gz"
 SOURCE_SAMTOOLS="https://github.com/samtools/samtools/archive/0.1.19.tar.gz"
 
 done_message () {
@@ -35,14 +31,7 @@ if [ "$#" -ne "1" ] ; then
   exit 0
 fi
 
-CPU=`grep -c ^processor /proc/cpuinfo`
-if [ $? -eq 0 ]; then
-  if [ "$CPU" -gt "6" ]; then
-    CPU=6
-  fi
-else
-  CPU=1
-fi
+CPU=`cat /proc/cpuinfo | egrep "^processor" | wc -l`
 echo "Max compilation CPUs set to $CPU"
 
 INST_PATH=$1
@@ -124,63 +113,14 @@ fi
 
 if [[ ",$COMPILE," == *,biobambam,* ]] ; then
   unset PERL5LIB
-  echo -n "Building snappy ..."
-  if [ -e $SETUP_DIR/snappy.success ]; then
-    echo -n " previously installed ..."
-  else
-    (
-      get_distro "snappy" $SOURCE_SNAPPY
-      cd $SETUP_DIR/snappy
-      ./configure --prefix=$INST_PATH
-      make -j$CPU
-      make -j$CPU install
-      touch $SETUP_DIR/snappy.success
-    ) >>$INIT_DIR/setup.log 2>&1
-  fi
-  done_message "" "Failed to build snappy."
-
-  echo -n "Building io_lib ..."
-  if [ -e $SETUP_DIR/io_lib.success ]; then
-    echo -n " previously installed ... "
-  else
-    (
-      get_distro "io_lib" $SOURCE_IOLIB
-      cd $SETUP_DIR/io_lib
-      ./configure --prefix=$INST_PATH
-      make -j$CPU
-      make -j$CPU install
-      touch $SETUP_DIR/io_lib.success
-    ) >>$INIT_DIR/setup.log 2>&1
-  fi
-  done_message "" "Failed to build io_lib."
-
-  echo -n "Building libmaus ..."
-  if [ -e $SETUP_DIR/libmaus.success ]; then
-    echo -n " previously installed ..."
-  else
-    (
-      get_distro "libmaus" $SOURCE_LIBMAUS
-      cd $SETUP_DIR/libmaus
-      autoreconf -i -f
-      ./configure --prefix=$INST_PATH --with-snappy=$INST_PATH --with-io_lib=$INST_PATH
-      make -j$CPU
-      make -j$CPU install
-      touch $SETUP_DIR/libmaus.success
-    ) >>$INIT_DIR/setup.log 2>&1
-  fi
-  done_message "" "Failed to build libmaus."
-
   echo -n "Building biobambam ..."
   if [ -e $SETUP_DIR/biobambam.success ]; then
     echo -n " previously installed ..."
   else
     (
-      get_distro "biobambam" $SOURCE_BIOBAMBAM
-      cd $SETUP_DIR/biobambam
-      autoreconf -i -f
-      ./configure --with-libmaus=$INST_PATH --prefix=$INST_PATH
-      make -j$CPU
-      make -j$CPU install
+      cd $SETUP_DIR
+      $INIT_DIR/bin/build_biobambam_relocatable.sh
+      cp -r biobambam/* $INST_PATH/.
       touch $SETUP_DIR/biobambam.success
     ) >>$INIT_DIR/setup.log 2>&1
   fi

t/3_external_progs.t

@@ -17,15 +17,15 @@ my %EXPECTED_VERSION = (
                         'bamcollate2'       => {
                               'get'   => q{ -h},
                               'match' => qr/This is biobambam version ([[:digit:]\.]+)\./,
-                              'version'       => ['0.0.147']},
+                              'version'       => ['0.0.148']},
                         'bammarkduplicates' => {
                               'get'   => q{ -h},
                               'match' => qr/This is biobambam version ([[:digit:]\.]+)\./,
-                              'version'       => ['0.0.147']},
+                              'version'       => ['0.0.148']},
                         'bamsort'           => {
                               'get'   => q{ -h},
                               'match' => qr/This is biobambam version ([[:digit:]\.]+)\./,
-                              'version'       => ['0.0.147']},
+                              'version'       => ['0.0.148']},
                         'bwa'           => {
                               'get'   => q{},
                               'match' => qr/Version: ([[:digit:]\.]+[[:alpha:]]?)/, # we don't care about the revision number