Merge branch 'hotfix/v3.3.2'

CHANGES.md

@@ -1,14 +1,22 @@
 # CHANGES
 
+## 3.3.2
+
+* Actually get the new `htslib` and `samtools` links correct in `setup.sh`
+* Move `samtools` install in `setup.sh` to happen before `Bio::DB::HTS`
+
 ## 3.3.1
+
 * `samtools` and `htslib` updated to 1.7
 * `Bio::DB::HTS` updated to 2.10, fixes error with GRCh38 contig names in Tabix.
 * Update tabix query to use `query_full`
 
 ## 3.3.0
+
 * Complete re-write of the reference generation code
 
 ## 3.2.2
+
 * Add bedtools2 to `setup.sh`
 * Added bedtools2 to `README.md`
 * Changes `Bio::DB::HTS`, `samtools` and `HTSlib` install methods.
@@ -17,15 +25,18 @@
 same start coord are sorted in a stable way.
 
 ## 3.2.0
+
 * Allows use of ensemblgenomes.org as a datasource
 * Handle genes without names, and give more useful error message
 * Ensure an error code is emmitted on failure
 
 ## 3.1.0
+
 * Adds travis testing
 * Cleans up install script and adds multi versioned paths to options
 
 ## 3.0.0
+
 * Removed use of legacy Tabix codebase and switches to samtools 1.2+
 * Switches to gihub version of vcftools and makes several patches unnecessary
 * Several bugfixes

lib/Sanger/CGP/Vagrent.pm

@@ -26,7 +26,7 @@ use strict;
 use Const::Fast qw(const);
 
 use base 'Exporter';
-our $VERSION = '3.3.1';
+our $VERSION = '3.3.2';
 our @EXPORT = qw($VERSION);
 
 1;

setup.sh

@@ -21,8 +21,8 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 ##########LICENCE##########
 
-SOURCE_SAMTOOLS="https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.7.tar.bz2"
-SOURCE_HTSLIB="https://github.com/samtools/htslib/releases/download/1.3.2/htslib-1.7.tar.bz2"
+SOURCE_SAMTOOLS="https://github.com/samtools/htslib/releases/download/1.7/htslib-1.7.tar.bz2"
+SOURCE_HTSLIB="https://github.com/samtools/samtools/releases/download/1.7/samtools-1.7.tar.bz2"
 SOURCE_BIOBDHTS="https://github.com/Ensembl/Bio-HTS/archive/2.10.tar.gz"
 SOURCE_VCFTOOLS="https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz"
 # Warning bedtools 2.24.0 and 2.25.0 have a swapped usage in coverageBed
@@ -119,16 +119,20 @@ cd $SETUP_DIR
 
 ## grab cpanm and stick in workspace, then do a self upgrade into bin:
 get_file $SETUP_DIR/cpanm https://cpanmin.us/
-perl $SETUP_DIR/cpanm -l $INST_PATH App::cpanminus
+perl $SETUP_DIR/cpanm --no-wget -l $INST_PATH App::cpanminus
 CPANM=`which cpanm`
 echo $CPANM
 
-perlmods=( "File::ShareDir" "File::ShareDir::Install" "Module::Build" "Bio::Root::[email protected]")
-
-for i in "${perlmods[@]}" ; do
-  echo -n "Installing build prerequisite $i..."
-  $CPANM --notest --mirror http://cpan.metacpan.org -l $INST_PATH $i
-done
+if [ -e $SETUP_DIR/basePerlDeps.success ]; then
+  echo "Previously installed base perl deps..."
+else
+  perlmods=( "File::ShareDir" "File::ShareDir::Install" "Module::Build" "Bio::Root::[email protected]")
+  for i in "${perlmods[@]}" ; do
+    echo -n "Installing build prerequisite $i..."
+    $CPANM --no-wget --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH $i
+  done
+  touch $SETUP_DIR/basePerlDeps.success
+fi
 
 echo -n "Building bedtools2 ..."
 if [ -e $SETUP_DIR/bedtools.success ]; then
@@ -162,6 +166,7 @@ else
   touch $SETUP_DIR/$CURR_TOOL.success
 fi
 
+echo -n "Get htslib ..."
 if [ -e $SETUP_DIR/htslibGet.success ]; then
   echo " already staged ...";
 else
@@ -188,6 +193,27 @@ fi
 
 export HTSLIB=$INST_PATH
 
+cd $INIT_DIR
+
+echo -n "Building samtools ..."
+if [ -e $SETUP_DIR/samtools.success ]; then
+  echo " previously installed ...";
+else
+echo
+  cd $SETUP_DIR
+  rm -rf samtools
+  get_distro "samtools" $SOURCE_SAMTOOLS
+  mkdir -p samtools
+  tar --strip-components 1 -C samtools -xjf samtools.tar.bz2
+  cd samtools
+  ./configure --enable-plugins --enable-libcurl --with-htslib=$HTSLIB --prefix=$INST_PATH
+  make -j$CPU all
+  make install
+  cd $SETUP_DIR
+  rm -f samtools.tar.bz2
+  touch $SETUP_DIR/samtools.success
+fi
+
 CHK=`perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' Bio::DB::HTS`
 if [[ "x$CHK" == "x" ]] ; then
   echo -n "Building Bio::DB::HTS ..."
@@ -198,9 +224,11 @@ if [[ "x$CHK" == "x" ]] ; then
     cd $SETUP_DIR
     rm -rf bioDbHts
     get_distro "bioDbHts" $SOURCE_BIOBDHTS
+    mkdir -p bioDbHts
     tar --strip-components 1 -C bioDbHts -zxf bioDbHts.tar.gz
     cd bioDbHts
-    perl Build.PL --install_base=$INST_PATH --htslib=$INST_PATH
+    perl Build.PL --htslib=$HTSLIB --install_base=$INST_PATH
+    ./Build
     ./Build test
     ./Build install
     cd $SETUP_DIR
@@ -211,24 +239,6 @@ else
   echo "Bio::DB::HTS already installed ..."
 fi
 
-if [ -e $SETUP_DIR/samtools.success ]; then
-  echo " previously installed ...";
-else
-echo
-  cd $SETUP_DIR
-  rm -rf samtools
-  get_distro "samtools" $SOURCE_SAMTOOLS
-  mkdir -p samtools
-  tar --strip-components 1 -C samtools -xjf samtools.tar.bz2
-  cd samtools
-  ./configure --enable-plugins --enable-libcurl --with-htslib=$HTSLIB --prefix=$INST_PATH
-  make -j$CPU all
-  make install
-  cd $SETUP_DIR
-  rm -f samtools.tar.bz2
-  touch $SETUP_DIR/samtools.success
-fi
-
 cd $INIT_DIR
 
 echo -n "Installing Perl prerequisites ..."