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Merge pull request #532 from wtsi-npg/devel
merge from devel to create release 65.0
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,20 @@ | ||
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| if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then | ||
| wget -q -w 30 https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh; | ||
| else | ||
| wget -q -w 30 https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; | ||
| fi | ||
|
|
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| /bin/bash miniconda.sh -b -p "$HOME/miniconda" | ||
| export PATH="$HOME/miniconda/bin:$PATH" | ||
| hash -r | ||
|
|
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| conda config --set always_yes yes | ||
| conda config --set changeps1 no | ||
| conda config --set show_channel_urls true | ||
| conda update -q conda | ||
|
|
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| conda config --add channels $CONDA_CHANNEL | ||
|
|
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| # Useful for debugging any issues with conda | ||
| conda info -a |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,141 +1,6 @@ | ||
| use strict; | ||
| use warnings; | ||
| use npg_tracking::util::build; | ||
|
|
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| my $class = npg_tracking::util::build->subclass(code => <<'EOF'); | ||
| use strict; | ||
| use warnings; | ||
| use File::Path qw(make_path remove_tree); | ||
| use File::Which qw(which); | ||
| 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 | ||
| use WTSI::DNAP::Utilities::Build; | ||
|
|
||
| my $requires = { | ||
| 'autodie' => 0, | ||
|
|
@@ -159,21 +24,21 @@ 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, | ||
|
|
@@ -202,6 +67,7 @@ my $requires = { | |
| 'POSIX' => 0, | ||
| 'Readonly' => 0, | ||
| 'Readonly::XS' => 0, | ||
| 'REST::Client' => 0, | ||
| 'Statistics::Lite' => 0, | ||
| 'strict' => 0, | ||
| 'Try::Tiny' => 0, | ||
|
|
@@ -215,7 +81,6 @@ my $requires = { | |
| 'npg_common::fastqcheck' => 0, | ||
| 'npg_common::roles::software_location' => 0, | ||
| 'npg_common::sequence::reference::base_count' => 0, | ||
| 'npg_testing::db' => 0, | ||
| 'npg_tracking::data::reference::list' => 0, | ||
| 'npg_tracking::data::bait::find' => 0, | ||
| 'npg_tracking::data::snv::find' => 0, | ||
|
|
@@ -261,17 +126,16 @@ my $build_requires = { | |
| 'npg_testing::db' => 0 | ||
| }; | ||
|
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| my $builder = $class->new( | ||
| my $builder = WTSI::DNAP::Utilities::Build->new( | ||
|
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| 'module_name' => 'npg_qc', | ||
| 'dist_author' => q(npg <[email protected]>), | ||
| 'dist_version' => $class->git_tag(), | ||
| 'dist_author' => q(wtsi-npg <[email protected]>), | ||
| 'dist_version' => WTSI::DNAP::Utilities::Build->git_tag(), | ||
| 'dist_abstract' => 'Illumina and WTSI quality control for Illumina sequencing data', | ||
| 'license' => 'gpl', | ||
|
|
||
| 'configure_requires' => { | ||
| 'ExtUtils::CBuilder' => 0, | ||
| 'npg_tracking::util::build' => 0, | ||
| 'WTSI::DNAP::Utilities::Build' => 0, | ||
| }, | ||
|
|
||
| 'build_requires' => $build_requires, | ||
|
|
||
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