[med-svn] [Git][med-team/bio-tradis][master] 3 commits: support samtools >= 1.10
Michael R. Crusoe
gitlab at salsa.debian.org
Wed Dec 25 13:54:32 GMT 2019
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 <michael.crusoe at gmail.com> 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 <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>
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 <michael.crusoe at gmail.com>
+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 <michael.crusoe at gmail.com>
+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
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