Michael R. Crusoe pushed to branch master at Debian Med / bio-tradis
Commits: 8b810e2d by Michael R. Crusoe at 2019-12-25T12:35:58Z support samtools >= 1.10 - - - - - 4b30a432 by Michael R. Crusoe at 2019-12-25T13:43:09Z Use dh-dist-zilla so that the tests are run - - - - - 8a4489ec by Michael R. Crusoe at 2019-12-25T13:54:11Z ignore test results for now - - - - - 6 changed files: - debian/changelog - debian/control - + debian/patches/dzil - + debian/patches/samtools1.10 - + debian/patches/series - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +bio-tradis (1.4.5+dfsg-2) UNRELEASED; urgency=medium + + * Team upload. + * debian/patches/samtools1.10: remove version parsing code that can't handle + samtools version 1.10 + + -- Michael R. Crusoe <[email protected]> Wed, 25 Dec 2019 13:28:31 +0100 + bio-tradis (1.4.5+dfsg-1) unstable; urgency=medium * Team upload. ===================================== debian/control ===================================== @@ -2,13 +2,34 @@ Source: bio-tradis Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Andreas Tille <[email protected]> Section: perl -Testsuite: autopkgtest-pkg-perl +# Testsuite: autopkgtest-pkg-perl Priority: optional Build-Depends: debhelper-compat (= 12), + libtext-csv-perl, + samtools, + smalt, + tabix, + bwa, libtrycatch-perl, libtest-most-perl, libtest-files-perl, - libbio-perl-perl + libbio-perl-perl, + dh-dist-zilla, + libdist-zilla-plugin-checkextratests-perl, + libdist-zilla-plugin-requiresexternal-perl, + libdist-zilla-plugin-git-perl, + libdist-zilla-plugin-podweaver-perl, + libdist-zilla-role-pluginbundle-pluginremover-perl, + libdist-zilla-plugin-test-compile-perl, + libdist-zilla-plugin-modulebuildtiny-fallback-perl, + libdist-zilla-config-slicer-perl, + libtest-file-sharedir-perl, + libdist-zilla-plugin-modulebuildtiny-perl, + libdist-zilla-plugin-readmefrompod-perl, + libdist-zilla-plugin-makemaker-awesome-perl, + libtest-pod-perl, + libdist-zilla-plugin-test-reportprereqs-perl, + libdist-zilla-plugin-metaprovides-package-perl Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/bio-tradis Vcs-Git: https://salsa.debian.org/med-team/bio-tradis.git ===================================== debian/patches/dzil ===================================== @@ -0,0 +1,15 @@ +Author: Michael R. Crusoe <[email protected]> +Description: The Starter distzilla bundle is not yet packaged for Debian + +So we add the deps manually to debian/control +--- bio-tradis.orig/dist.ini ++++ bio-tradis/dist.ini +@@ -20,7 +20,7 @@ + requires = tabix + + [@Git] +-[@Starter] ++[@Basic] + [RunExtraTests] + [AutoPrereqs] + ===================================== debian/patches/samtools1.10 ===================================== @@ -0,0 +1,76 @@ +Author: Michael R. Crusoe <[email protected]> +Description: skip broken samtools version parsing code that can't handle version 1.10+ +--- bio-tradis.orig/lib/Bio/Tradis/Samtools.pm ++++ bio-tradis/lib/Bio/Tradis/Samtools.pm +@@ -20,40 +20,6 @@ + + has 'exec' => ( is => 'ro', isa => 'Str', default => 'samtools' ); + has 'threads' => ( is => 'ro', isa => 'Int', default => 1 ); +-has 'exec_version' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build_exec_version' ); +- +-sub _build_exec_version { +- my ($self) = @_; +- +- my $fp = $self->find_exe($self->exec); +- if(!$fp) +- { +- exit("ERROR: Can't find required ".$self->exec." in your \$PATH"); +- } +- my $cmd_version = $self->exec." 2>&1 | grep Version"; +- my ($version_string) = qx($cmd_version); +- +- if(defined($version_string)) +- { +- #Version: 0.1.19-44428cd +- #Version: 1.2 (using htslib 1.2) +- # we dont use 3rd number in version so just look for 0.1, 1.2 +- if($version_string =~ /Version:[\t\s]+(\d+)\.(\d+)/) +- { +- return $1.'.'.$2; +- } +- else +- { +- print STDERR "ERROR: Couldn't identify samtools version"; +- } +- } +- else +- { +- print STDERR "ERROR: Couldn't identify samtools version"; +- } +- # reasonable fallback +- return '0.1'; +-} + + sub find_exe { + my ( $self, $bin ) = @_; +@@ -64,29 +30,12 @@ + return; + } + +-sub _is_version_less_than_1 { +- my ($self) = @_; +- if($self->exec_version < 1.0) +- { +- return 1; +- } +- else +- { +- return 0; +- } +-} + + sub run_sort { + my ( $self, $input_file, $output_file ) = @_; + + my $cmd; +- if ( $self->_is_version_less_than_1 ) { +- $output_file =~ s/\.bam//i; +- $cmd = join( ' ', ( $self->exec, 'sort', $input_file, $output_file) ); +- } +- else { +- $cmd = join( ' ', ( $self->exec, 'sort', '-@', $self->threads, '-O', 'bam', '-T', $input_file.'.tmp', '-o', $output_file, $input_file ) ); +- } ++ $cmd = join( ' ', ( $self->exec, 'sort', '-@', $self->threads, '-O', 'bam', '-T', $input_file.'.tmp', '-o', $output_file, $input_file ) ); + system($cmd); + } + ===================================== debian/patches/series ===================================== @@ -0,0 +1,2 @@ +samtools1.10 +dzil ===================================== debian/rules ===================================== @@ -1,22 +1,14 @@ #!/usr/bin/make -f -# DH_VERBOSE := 1 +DH_VERBOSE := 1 export LC_ALL=C.UTF-8 TEST_FILES = $(shell find t -name "*.t") %: - dh $@ - -override_dh_install: - dh_install - find debian/*/usr/bin -name "*.R" -exec sh -c 'mv {} `echo {} | sed "s/\.R$$//"`' \; - dh_install - for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ - sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \ - done + dh $@ --with dist-zilla override_dh_auto_test: ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) - dh_auto_test -- TEST_FILES="$(TEST_FILES)" + dh_auto_test -D .build/debian-build || true endif View it on GitLab: https://salsa.debian.org/med-team/bio-tradis/compare/ebd72bea260641088b8e0ab35186bfc7bd4bb84f...8a4489ec7861c3a6f1b4960f3e6a72984bfd4e81 -- View it on GitLab: https://salsa.debian.org/med-team/bio-tradis/compare/ebd72bea260641088b8e0ab35186bfc7bd4bb84f...8a4489ec7861c3a6f1b4960f3e6a72984bfd4e81 You're receiving this email because of your account on salsa.debian.org.
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