Merge pull request #520 from keithj/remove-c-src

Removed C utilities, replaced from Conda channel.

.travis.yml

@@ -32,25 +32,29 @@ env:
     - TRAVIS_NODE_VERSION="6.12.2"
     - TRAVIS_NPM_VERSION="4.5.0"
     - TRAVIS_YARN_VERSION="1.3.2"
+    - TRAVIS_PYTHON_VERSION="2.7"
     - WTSI_NPG_GITHUB_URL=https://github.com/wtsi-npg
     - IRODS_VERSION=4.1.10 PG_PLUGIN_VERSION=1.10 PLATFORM=ubuntu12
+    - CONDA_CHANNEL=https://dnap.cog.sanger.ac.uk/npg/conda/test/Ubuntu/12.04/
+    - CONDA_TEST_ENV=test-environment
 
 before_install:
   # workaround for iRODS buffer overflow
   # see https://github.com/travis-ci/travis-ci/issues/5227
   - sudo hostname "$(hostname | cut -c1-63)"
   - sed -e "s/^\\(127\\.0\\.0\\.1.*\\)/\\1 $(hostname | cut -c1-63)/" /etc/hosts > /tmp/hosts
   - sudo mv /tmp/hosts /etc/hosts
+  - ./.travis/before_install_conda.sh
   - ./.travis/before_install_mysql57.sh
   - ./.travis/before_install.sh
 
 install:
   - ./.travis/install.sh
 
 script:
-  - export PATH=$IRODS_RIP_DIR/iRODS/clients/icommands/bin:$PATH
   - ienv
   - ils
   - ilsresc -l
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - source activate "$CONDA_TEST_ENV"
   - ./.travis/script.sh
-

.travis/before_install_conda.sh

@@ -0,0 +1,20 @@
+
+if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+    wget -q -w 30 https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
+else
+    wget -q -w 30 https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+fi
+
+/bin/bash miniconda.sh -b -p "$HOME/miniconda"
+export PATH="$HOME/miniconda/bin:$PATH"
+hash -r
+
+conda config --set always_yes yes
+conda config --set changeps1 no
+conda config --set show_channel_urls true
+conda update -q conda
+
+conda config --add channels $CONDA_CHANNEL
+
+# Useful for debugging any issues with conda
+conda info -a

.travis/before_install_mysql57.sh

@@ -13,12 +13,12 @@ sudo rm -rf /var/log/mysql
 
 # Get packages from oracle
 sudo -E apt-get install libaio1 apparmor
-wget http://downloads.mysql.com/archives/get/file/mysql-common_5.7.13-1ubuntu12.04_amd64.deb
-wget http://downloads.mysql.com/archives/get/file/libmysqlclient20_5.7.13-1ubuntu12.04_amd64.deb
-wget http://downloads.mysql.com/archives/get/file/mysql-community-client_5.7.13-1ubuntu12.04_amd64.deb
-wget http://downloads.mysql.com/archives/get/file/mysql-client_5.7.13-1ubuntu12.04_amd64.deb
-wget http://downloads.mysql.com/archives/get/file/mysql-community-server_5.7.13-1ubuntu12.04_amd64.deb
-wget http://downloads.mysql.com/archives/get/file/mysql-server_5.7.13-1ubuntu12.04_amd64.deb
+wget -q http://downloads.mysql.com/archives/get/file/mysql-common_5.7.13-1ubuntu12.04_amd64.deb
+wget -q http://downloads.mysql.com/archives/get/file/libmysqlclient20_5.7.13-1ubuntu12.04_amd64.deb
+wget -q http://downloads.mysql.com/archives/get/file/mysql-community-client_5.7.13-1ubuntu12.04_amd64.deb
+wget -q http://downloads.mysql.com/archives/get/file/mysql-client_5.7.13-1ubuntu12.04_amd64.deb
+wget -q http://downloads.mysql.com/archives/get/file/mysql-community-server_5.7.13-1ubuntu12.04_amd64.deb
+wget -q http://downloads.mysql.com/archives/get/file/mysql-server_5.7.13-1ubuntu12.04_amd64.deb
 sudo debconf-set-selections <<< "mysql-server mysql-server/root_password password \"''\""
 sudo debconf-set-selections <<< "mysql-server mysql-server/root_password_again password \"''\""
 sudo dpkg-preconfigure mysql-community-server_5.7.13-1ubuntu12.04_amd64.deb  

.travis/install.sh

@@ -16,7 +16,6 @@ WTSI_NPG_BUILD_BRANCH=${WTSI_NPG_BUILD_BRANCH:=$TRAVIS_BRANCH}
 IRODS_RIP_DIR=${IRODS_RIP_DIR:+$IRODS_RIP_DIR}
 
 sudo apt-get install libgd2-xpm-dev # For npg_tracking
-sudo apt-get install liblzma-dev # For npg_qc
 
 # CPAN as in npg_npg_deploy
 cpanm --notest --reinstall App::cpanminus
@@ -26,6 +25,11 @@ cpanm --quiet --notest Alien::Tidyp
 cpanm --quiet --notest LWP::Protocol::https
 cpanm --quiet --notest https://github.com/chapmanb/vcftools-cpan/archive/v0.953.tar.gz
 
+# Conda
+export PATH="$HOME/miniconda/bin:$PATH"
+conda create -q --name "$CONDA_TEST_ENV" python=$TRAVIS_PYTHON_VERSION
+conda install --name "$CONDA_TEST_ENV" npg_qc_utils
+
 # iRODS
 wget -q https://github.com/wtsi-npg/disposable-irods/releases/download/${DISPOSABLE_IRODS_VERSION}/disposable-irods-${DISPOSABLE_IRODS_VERSION}.tar.gz -O /tmp/disposable-irods-${DISPOSABLE_IRODS_VERSION}.tar.gz
 tar xfz /tmp/disposable-irods-${DISPOSABLE_IRODS_VERSION}.tar.gz -C /tmp

Build.PL

@@ -10,131 +10,16 @@ my $class = npg_tracking::util::build->subclass(code => <<'EOF');
   use npg_tracking::util::abs_path qw(abs_path);
   use File::Basename;
 
-  my $C_SOURCE_DIR = q[src];
-
-  my $c_tools = {};
-
-  if (which('lsb_release') and `lsb_release -a` =~ /precise/ismx) {
-    $c_tools->{'fastq_summ'} = {'copy'     => [qw/fastq_summ/],
-                                'samtools' => 1};
-    $c_tools->{'fastqcheck'} = {'copy'     => [qw/fastqcheck/],
-                                'samtools' => 1};
-    $c_tools->{'gt_utils'} = {'copy'     => [qw/find_gt_match gt_pack/], };
-    $c_tools->{'norm_fit'} = {'copy'     => [qw/norm_fit/], };
-  }
-
-  sub _c_build_dir {
-    return join(q[/], $C_SOURCE_DIR, shift, 'build');
-  }
-
-  sub _c_src_dir {
-    return join(q[/], $C_SOURCE_DIR, shift);
-  }
-
-  sub _samtools_option {
-    my $self = shift;
-
-    my ($samtools, $htslib);
-
-    # Requires the samtools source code to build
-    if ($ENV{SAMTOOLS_SOURCE_PATH}) {
-      $samtools = $ENV{SAMTOOLS_SOURCE_PATH};
-    } else {
-      $samtools = _relative_to_bin('samtools')
-    }
-
-    if ($ENV{HTSLIB_INSTALL_PATH}) {
-      $htslib = $ENV{HTSLIB_INSTALL_PATH};
-    } else {
-      $htslib = _relative_to_bin('htsfile')
-    }
-
-    my @pkgs;
-    if ($samtools && $htslib) {
-      push @pkgs, "SAMTOOLS_LOC=$samtools";
-      push @pkgs, "HTSLIB_LOC=$htslib";
-
-      if ($self->verbose) {
-        warn "Found samtools source $samtools\n";
-        warn "Found htslib installed $htslib\n";
-      }
-    }
-
-    return \@pkgs;
-  }
-
-  sub _relative_to_bin {
-    my ($executable) = @_;
-
-    my $path;
-    my @found = which($executable);
-    if (@found) {
-      $path = dirname abs_path($found[0]);
-      if ($path =~ m{/bin\Z}smx) {
-        $path = dirname $path;
-      }
-    }
-
-    return $path;
-  }
-
   sub ACTION_build {
     my $self = shift;
     $self->SUPER::ACTION_build;
 
-    # Build C executables
-    foreach my $tool ( keys %{$c_tools} ) {
-      if ($self->verbose) {
-        warn "Building $tool\n";
-      }
-      my $bdir = _c_build_dir($tool);
-      make_path $bdir;
-      my $silent = $self->verbose ? q[] : '--silent';
-      my $extra_info = q[];
- 
-      if ($c_tools->{$tool}->{'samtools'}) {
-        my @pkgs = @{$self->_samtools_option()};
-        if (!@pkgs) {
-          warn 'samtools and htslib locations not declared or detected, ' .
-                 "skipping $tool build\n";
-          next;
-        }
-        $extra_info = join q[ ], @pkgs;
-      }
-
-      my $command = sprintf 'make %s --directory %s %s',
-                      $silent, _c_src_dir($tool), $extra_info;
-      if (system $command) {
-        die "Failed to compile $tool";
-      }
-      foreach my $ename ( @{$c_tools->{$tool}->{'copy'}} ) {
-        $self->copy_if_modified(
-          from    => join(q[/], $bdir, $ename),
-          to_dir  => join(q[/], $self->base_dir(), $self->blib(), 'script'),
-          flatten => 1);
-      }
-    }
-
     # Build R script
     $self->copy_if_modified(
       from    => 'lib/R/gc_bias_data.R',
       to_dir  => join(q[/], $self->base_dir(), $self->blib()),
       flatten => 0);
   }
-
-  sub ACTION_clean {
-    my $self = shift;
-    $self->SUPER::ACTION_clean;
-
-    foreach my $tool ( keys %{$c_tools} ) {
-      if ($self->verbose) {
-        warn "Cleaning $tool\n";
-      }
-      my $silent = $self->verbose ? q[] : '--silent';
-      system "make clean $silent --directory " . _c_src_dir($tool);
-      remove_tree _c_build_dir($tool);
-    }
-  }
 EOF
 
 my $requires = {
@@ -159,21 +44,21 @@ my $requires = {
                 'Fcntl'                           => 0,
                 'File::Basename'                  => 0,
                 'File::Glob'                      => 0,
-                'File::Path'                      => 0, 
+                'File::Path'                      => 0,
                 'File::Spec'                      => 0,
                 'File::Spec::Functions'           => 0,
                 'File::Slurp'                     => 0,
                 'File::Temp'                      => 0,
                 'FindBin'                         => '1.47',
                 'Getopt::Long'                    => '2.37',
-                'Getopt::Std'                     => 0,           
-                'HTTP::Request'                   => 0,          
+                'Getopt::Std'                     => 0,
+                'HTTP::Request'                   => 0,
                 'IPC::SysV'                       => 0,
                 'IO::Compress::Xz'                => '2.068',
                 'IO::Uncompress::UnXz'            => '2.068',
                 'JSON'                            => '2.12',
                 'JSON::XS'                        => 0,
-                'lib'                             => 0,            
+                'lib'                             => 0,
                 'List::MoreUtils'                 => 0,
                 'List::Util'                      => 0,
                 'LWP::UserAgent'                  => 0,

MANIFEST

@@ -173,22 +173,6 @@ lib/R/gc_bias_data.R
 MANIFEST
 README
 scripts/npgqc_dbix_schema_loader.pl
-src/fastq_summ/Makefile
-src/fastq_summ/fastq_summ.c
-src/fastq_summ/fastqcheck.c
-src/fastq_summ/fastqcheck.h
-src/gt_utils/Makefile
-src/gt_utils/README
-src/gt_utils/find_gt_match.c
-src/gt_utils/fld_desc.c
-src/gt_utils/fld_desc.h
-src/gt_utils/gt_pack.c
-src/gt_utils/gt_pack.h
-src/gt_utils/intvec.c
-src/gt_utils/intvec.h
-src/window_depth.d
-src/norm_fit/Makefile
-src/norm_fit/norm_fit.c
 t/00-critic.t
 t/00-distribution.t
 t/00-podcoverage.t

README

@@ -18,7 +18,7 @@ scripts directory:
 
 src directory:
 --------------
- source code for C utilities
+ Moved to https://github.com/wtsi-npg/npg_qc_utils
 
 t directory:
 ------------