Changes for release 1.14.0

doc/CHANGELOG.md

@@ -4,12 +4,70 @@ Change log for WTSI genotyping pipeline
 
 Latest version is hosted at: https://github.com/wtsi-npg/genotyping
 
-Unreleased
-----------
+Release 1.14.0: 2017-02-07
+--------------------------
+
+Added:
+- Gencall workflow:
+  - Writes Plink data and runs QC for Gencall only
+  - New option in ready_workflow.pl
+- Replace old identity metric with new Bayesian version, which will:
+   - Appear in main QC output and plots
+   - Contribute to sample pass/fail status
+
+Changed:
+- Extensive refactoring of Collation.pm, to make it more maintainable
+and support Log4Perl. Module renamed Collator.pm and changed into a
+Moose class.
+
+Fixed:
+- Check for allowed combination of plex manifests and VCF files in
+workflow arguments (Issue #434) 
+- Create Text::CSV objects with binary flag enabled (Issue #406)
+
+
+Release 1.13.2: 2016-11-10
+--------------------------
+
+Changed:
+- Hotfix: Add cgp and ddd references to WTSI::NPG::Genotyping::QC::Identity
+
+
+Release 1.13.1: 2016-07-28 
+--------------------------
+
+Changed:
+- Made install.sh more transparent and portable.
+- Updated WTSI-DNAP-Utilities and perl-irods-wrap versions in install.sh.
+
+Fixed:
+- Default LSF queue for Ruby workflows
+
+
+Release 1.13.0: 2016-06-20
+--------------------------
 
 Added:
-- Replace old identity check with new Bayesian version in "main" QC output
-and plots
+- install.sh script to install pipeline and its Perl dependencies
+- Documentation for Bayesian identity check
+
+Changed:
+- Modified ready_workflow.pl to better align with user SOP
+- Use try/catch to handle unexpected errors in retrieving QC plex results
+from iRODS
+- Updated reference genome for Sequenom iRODS query
+- Update perl-irods-wrap dependency to 2.4.0; removes unhelpful warning
+messages to STDERR. This in turn requires baton version >= 0.16.4.
+
+Removed:
+- Script publish_infinium_file_list.pl; superseded by other publish scripts
+
+
+Release 1.12.1: 2016-05-13
+--------------------------
+
+Fixed:
+- Support repeat scans from Infinium database
 
 
 Release 1.13.2: 2016-11-10

src/bash/cpanm.sha256

@@ -0,0 +1 @@
+9da50e155df72bce55cb69f51f1dbb4b62d23740fb99f6178bb27f22ebdf8a46  ./App-cpanminus-1.7042.tar.gz

src/bash/install.sh

@@ -8,26 +8,66 @@
 
 # similar in purpose to npg_irods/scripts/travis_install.sh
 
+set -e # script will exit if any command has a non-zero return value
+
+# check for environment variables
 if [ -z $INSTALL_ROOT ]; then
-    echo "INSTALL_ROOT environment variable must specify the path to a directory for installation; exiting." >&2
+    echo "Environment variable INSTALL_ROOT must specify directory path for installation; exiting." >&2
+    exit 1
+fi
+if [ -z $RUBY_HOME ]; then
+    echo "Required environment variable RUBY_HOME not set; exiting." 1>&2
+    exit 1
+fi
+if [ -z $GEM_PATH ]; then
+    echo "Required environment variable GEM_PATH not set; exiting." 1>&2
     exit 1
-elif [ ! -e $INSTALL_ROOT ]; then
-    echo "INSTALL_ROOT environment variable path $INSTALL_ROOT does not exist; exiting." >&2
+fi
+if [ -n $GEM_HOME ]; then
+    echo "Warning: Existing GEM_HOME variable '$GEM_HOME' will be changed to value of INSTALL_ROOT" 1>&2
+fi
+
+# test that INSTALL_ROOT is a writable directory
+if [ ! -e $INSTALL_ROOT ]; then
+    echo "INSTALL_ROOT environment variable path $INSTALL_ROOT does not exist; exiting." 1>&2
     exit 1
 elif [ ! -d $INSTALL_ROOT ]; then
-    echo "INSTALL_ROOT environment variable path $INSTALL_ROOT is not a directory; exiting." >&2
+    echo "INSTALL_ROOT environment variable path $INSTALL_ROOT is not a directory; exiting." 1>&2
+    exit 1
+elif  [ ! -w $INSTALL_ROOT ]; then
+    echo "INSTALL_ROOT environment variable path $INSTALL_ROOT is not writable; exiting." 1>&2
     exit 1
 else
     echo "Installing pipeline to root directory $INSTALL_ROOT"
 fi
 
-WTSI_DNAP_UTILITIES_VERSION="0.5.2"
+# set Ruby environment variables
+export PATH=$RUBY_HOME/bin:$PATH
+export MANPATH=$RUBY_HOME/share/man:$MANPATH
+export GEM_HOME=$INSTALL_ROOT
+# split GEM_PATH to find a bin directory
+IFS=':' # IFS = Bash "Internal Field Separator"
+GEM_ARRAY=($GEM_PATH)
+unset IFS
+GEM_BIN=${GEM_ARRAY[0]}/bin
+if [ ! -e $GEM_BIN ]; then
+    echo "Expected Ruby script directory '$GEM_BIN' does not exist" 1>&2
+    exit 1
+elif  [ ! -d $GEM_BIN ]; then
+    echo "Expected Ruby script directory '$GEM_BIN' is not a directory" 1>&2
+    exit 1
+fi
+export PATH=$GEM_BIN:$PATH
+# update GEM_PATH
+export GEM_PATH=$INSTALL_ROOT:$GEM_PATH
+
+# version numbers
+CPANM_VERSION="1.7042"
+WTSI_DNAP_UTILITIES_VERSION="0.5.3"
 ML_WAREHOUSE_VERSION="2.1"
 ALIEN_TIDYP_VERSION="1.4.7"
 NPG_TRACKING_VERSION="85.3"
 NPG_IRODS_VERSION="2.5.0"
-RUBY_VERSION="1.8.7-p330"
-LIB_RUBY_VERSION="0.3.0"
 
 START_DIR=$PWD
 
@@ -39,18 +79,46 @@ SRC_DIRS=($PERL_DIR $RUBY_DIR)
 for DIR in ${SRC_DIRS[@]}; do
     if [ ! -d $DIR ]; then
         echo -n "Genotyping source code directory $DIR not found; "
-        echo "install halted" >&2 
+        echo "install halted" 1>&2 
         exit 1
     fi
 done
 
+# ensure temporary directory is cleaned up (even after unexpected exit)
+function finish {
+    cd $START_DIR
+    rm -Rf $TEMP
+}
+trap finish EXIT
+
 # create and cd to temp directory
 TEMP_NAME=`mktemp -d genotyping_temp.XXXXXXXX`
 TEMP=`readlink -f $TEMP_NAME` # full path to temp directory
-CPANM_TEMP="$TEMP/cpanm"
-mkdir $CPANM_TEMP
-export PERL_CPANM_HOME=$CPANM_TEMP
-export PATH=$TEMP:$PATH # ensure cpanm download is on PATH
+export PERL_CPANM_HOME="$TEMP/cpanm_home"
+mkdir $PERL_CPANM_HOME
+mkdir "$TEMP/cpanm" # cpanm installation directory
+export PATH=$TEMP/cpanm/bin:$PATH # ensure cpanm download is on PATH
+cd $TEMP
+
+# Download, verify and install cpanm
+# See checksum at http://www.cpan.org/authors/id/M/MI/MIYAGAWA/CHECKSUMS
+CPANM_TARFILE=App-cpanminus-$CPANM_VERSION.tar.gz
+CPANM_URL=http://search.cpan.org/CPAN/authors/id/M/MI/MIYAGAWA/$CPANM_TARFILE
+wget $CPANM_URL
+sha256sum -c $SCRIPT_DIR/cpanm.sha256 # verify checksum of the cpanm download
+tar -xzf $CPANM_TARFILE
+cd App-cpanminus-$CPANM_VERSION
+perl Makefile.PL INSTALL_BASE=$TEMP/cpanm
+make
+make test
+make install
+CPANM_SCRIPT=$TEMP/cpanm/bin/cpanm
+if [ ! -e $CPANM_SCRIPT ]; then
+    echo "Cannot find cpanm script '$CPANM_SCRIPT'; install halted" 1>&2
+    exit 1 
+fi
+echo -n "cpanm script is $CPANM_SCRIPT, version: "
+$CPANM_SCRIPT --version
 cd $TEMP
 
 # use wget to download tarballs to install
@@ -62,17 +130,9 @@ https://github.com/wtsi-npg/perl-irods-wrap/releases/download/$NPG_IRODS_VERSION
 
 for URL in ${URLS[@]}; do
     wget $URL
-    if [ $? -ne 0 ]; then
-        echo -n "Failed to download $URL; non-zero exit status " >&2
-        echo " from wget; install halted" >&2
-        exit 1
-    fi
 done
 eval $(perl -Mlocal::lib=$INSTALL_ROOT) # set environment variables
 
-# use local installation of cpanm
-module load cpanm/1.7042
-
 # install prerequisites from tarfiles
 TARFILES=(WTSI-DNAP-Utilities-$WTSI_DNAP_UTILITIES_VERSION.tar.gz \
 ml_warehouse-$ML_WAREHOUSE_VERSION.tar.gz \
@@ -81,67 +141,28 @@ npg-tracking-$NPG_TRACKING_VERSION.tar.gz \
 WTSI-NPG-iRODS-$NPG_IRODS_VERSION.tar.gz)
 
 for FILE in ${TARFILES[@]}; do
-    cpanm --installdeps $FILE --self-contained  --notest
-    if [ $? -ne 0 ]; then
-        echo "cpanm --installdeps failed for $FILE; install halted" >&2
-        exit 1
-    fi
-    cpanm --install $FILE --notest
-    if [ $? -ne 0 ]; then
-        echo "cpanm --install failed for $FILE; install halted" >&2
-        exit 1
-    fi
+    $CPANM_SCRIPT --installdeps $FILE --self-contained  --notest
+    $CPANM_SCRIPT --install $FILE --notest
 done
 
 cd $PERL_DIR
 
-cpanm --installdeps . --self-contained --notest 
-if [ $? -ne 0 ]; then
-    echo "cpanm --installdeps failed for genotyping; install halted" >&2
-    exit 1
-fi
+$CPANM_SCRIPT --installdeps . --self-contained --notest
 
 perl Build.PL
 ./Build install --install_base $INSTALL_ROOT
-if [ $? -ne 0 ]; then
-    echo "Genotyping pipeline Perl installation failed; install halted " >&2
-    exit 1
-fi
 
-# now set Ruby environment variables and install
-if [ -z $RUBY_HOME ]; then
-    export RUBY_HOME=/software/gapi/pkg/ruby/$RUBY_VERSION
-fi
-export PATH=$RUBY_HOME/bin:$PATH
-export MANPATH=$RUBY_HOME/share/man:$MANPATH
-if [ -z $GEM_HOME ]; then
-    export GEM_HOME=$INSTALL_ROOT
-fi
-if [ -z $GEM_PATH ]; then
-    export GEM_PATH=/software/gapi/pkg/lib-ruby/$LIB_RUBY_VERSION
-fi
-export GEM_PATH=$INSTALL_ROOT:$GEM_PATH
-export PATH=$GEM_PATH/bin:$PATH
+echo "Perl installation complete; now installing Ruby."
 
 cd $RUBY_DIR
 GENOTYPING_GEM=`rake gem | grep File | cut -f 4 -d " "`
-if [ $? -ne 0 ]; then
-    echo "'rake gem' failed for genotyping; install halted" >&2
-    exit 1
-fi
 GEM_FILE_PATH=pkg/$GENOTYPING_GEM
 if [ ! -f $GEM_FILE_PATH ]; then
-    echo "Expected gem file '$GEM_FILE_PATH' not found; install halted" >&2
+    echo "Expected gem file '$GEM_FILE_PATH' not found; install halted" 1>&2
     exit 1
 fi
 gem install $GEM_FILE_PATH
-if [ $? -ne 0 ]; then
-    echo "'gem install' failed for genotyping; install halted" >&2
-    exit 1
-fi
 
-# clean up temporary directory
-cd $START_DIR
-rm -Rf $TEMP
+echo "Ruby installation complete."
 
 exit 0

src/perl/Build.PL

@@ -44,6 +44,7 @@ my $build = Build->new
                          'Text::CSV'                           => '>= 1.33',
                          'Try::Tiny'                           => '>= 0.22',
                          'URI'                                 => '>= 1.67',
+                         'WTSI::DNAP::Utilities'               => '>= 0.5.3',
                          'WTSI::DNAP::Warehouse::Schema'       => '>= 1.1',
                          'WTSI::NPG::iRODS'                    => '>= 2.1.0'
                         },