debian/bioperl-run.lintian-overrides

+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+bioperl-run: script-with-language-extension usr/bin/bp_bioperl_application_installer.pl
+bioperl-run: script-with-language-extension usr/bin/bp_multi_hmmsearch.pl
+bioperl-run: script-with-language-extension usr/bin/bp_panalysis.pl
+bioperl-run: script-with-language-extension usr/bin/bp_papplmaker.pl
+bioperl-run: script-with-language-extension usr/bin/bp_run_neighbor.pl
+bioperl-run: script-with-language-extension usr/bin/bp_run_protdist.pl

debian/changelog

-bioperl-run (1.7.2-4) UNRELEASED; urgency=medium
+bioperl-run (1.7.2-4) unstable; urgency=medium
 
   * (Build-)Depends: ncoils
   * do not run tests parallel to get sensibly sorted output
   * Allow MPI oversubscription (as in phyml build since phyml caused
     problems inside build time tests)
+    This is also not reliable - skip phyml test at all
     Closes: #906337
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Fix Homepage
+  * Lintian-override for script-with-language-extension
 
- -- Andreas Tille <tille@debian.org>  Fri, 14 Sep 2018 13:22:55 +0200
+ -- Andreas Tille <tille@debian.org>  Fri, 14 Sep 2018 20:10:08 +0200
 
 bioperl-run (1.7.2-3) unstable; urgency=medium
 

debian/compat

-10
+11

debian/control

@@ -5,7 +5,7 @@ Uploaders: Charles Plessy <plessy@debian.org>,
 Section: science
 Testsuite: autopkgtest-pkg-perl
 Priority: optional
-Build-Depends: debhelper (>= 10)
+Build-Depends: debhelper (>= 11~)
 Build-Depends-Indep: perl,
                      libmodule-build-perl,
                      bioperl,
@@ -48,10 +48,10 @@ Build-Depends-Indep: perl,
                      wise,
 # Needed for the network tests:
                      libwww-perl
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/git/debian-med/bioperl-run.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/bioperl-run.git
-Homepage: http://search.cpan.org/dist/BioPerl-Run/
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/bioperl-run
+Vcs-Git: https://salsa.debian.org/med-team/bioperl-run.git
+Homepage: https://metacpan.org/release/BioPerl-Run
 
 Package: bioperl-run
 Architecture: all

debian/patches/adjust_bowtie_tests.patch

-Description: adjust expected test output, bowtie-1.2.1+ returns 2000 processed
-reads instead of 1000
-From: Alex Mestiashvili <mailatgoogl@gmail.com>
---- bioperl-run.orig/t/Bowtie.t
-+++ bioperl-run/t/Bowtie.t
-@@ -185,14 +185,14 @@
-     ok $bowtiefac->_run( -ind => $refseq,
-                          -seq => $rda1,  -seq2 => $rda2 ), "read paired fasta sequence";
-     
--    like($bowtiefac->stderr, qr/reads processed: 1000/, "bowtie success");
-+    like($bowtiefac->stderr, qr/reads processed: 2000/, "bowtie success");
- 
-     $bowtiefac->reset_parameters( -fasta => 0 );
-     $bowtiefac->set_parameters( -fastq => 1 );
-     ok $bowtiefac->_run( -ind => $refseq,
-                          -seq => $rdq1,  -seq2 => $rdq2 ), "read paired fastq sequence";
-     
--    like($bowtiefac->stderr, qr/reads processed: 1000/, "bowtie success");
-+    like($bowtiefac->stderr, qr/reads processed: 2000/, "bowtie success");
-     
- 
-     # test single

debian/patches/hyphy.patch

@@ -17,7 +17,7 @@ Description: Hyphy
  BEGIN {
      use Bio::Root::Test;
 -    test_begin(-tests => 10,
-+    test_begin(-tests => 9,
++    test_begin(-tests => 6,
                 -requires_module =>'IO::String');
  
      use_ok('Bio::Tools::Run::Phylo::Hyphy::SLAC');

debian/patches/skip_tests_for_phyml.patch

@@ -35,7 +35,7 @@ Description: Somehow there are issues to initialise openmpi, but beside these wa
     *** on a NULL communicator
     *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
     ***    and potentially your MPI job)
-    [hostname:2001] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
+    [hostname:2001] Local abort before MPI_INIT completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
  .
 
 --- a/t/Phyml.t

debian/patches/skip_tests_for_samtools.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Update: Fri, 16 Dec 2016 09:17:37 +0100
-Description: May be this is just a result of samtools incompatibilities
-    ------------- EXCEPTION -------------
-MSG: /usr/bin/samtools call crashed: There was a problem running /usr/bin/samtools : [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
-Usage: samtools sort [options...] [in.bam]
-Options:
-  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)
-  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]
-  -n         Sort by read name
-  -o FILE    Write final output to FILE rather than standard output
-  -T PREFIX  Write temporary files to PREFIX.nnnn.bam
-  -@, --threads INT
-             Set number of sorting and compression threads [1]
-      --input-fmt-option OPT[=VAL]
-               Specify a single input file format option in the form
-               of OPTION or OPTION=VALUE
-  -O, --output-fmt FORMAT[,OPT[=VAL]]...
-               Specify output format (SAM, BAM, CRAM)
-      --output-fmt-option OPT[=VAL]
-               Specify a single output file format option in the form
-               of OPTION or OPTION=VALUE
-      --reference FILE
-               Reference sequence FASTA FILE [null]
-
-STACK Bio::Tools::Run::WrapperBase::_run /build/bioperl-run-1.6.9/blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm:1033
-STACK Bio::Tools::Run::Samtools::run /build/bioperl-run-1.6.9/blib/lib/Bio/Tools/Run/Samtools.pm:176
-STACK toplevel t/Samtools.t:103
-    -------------------------------------
-
---- a/t/Samtools.t
-+++ b/t/Samtools.t
-@@ -10,7 +10,7 @@ BEGIN {
-                       # '..' for debugging from .t file
-     unshift @INC, $home;
-     use Bio::Root::Test;
--    test_begin(-tests => 40,
-+    test_begin(-tests => 37,
- 	       -requires_modules => [qw(IPC::Run Bio::Tools::Run::Samtools)]);
- }
- 
-@@ -65,8 +65,8 @@ is_deeply( $samt->{_options}->{_prefixes
- is_deeply( $samt->{_options}->{_params}, 
- 	   [qw( command refseq map_qcap ref_list site_list theta n_haplos exp_hap_diff indel_prob )],
- 	   "commands filtered by prefix");
--is( join(' ', @{$samt->_translate_params}),
--    "pileup -T 0.05 -f my.fas", "translate params" );
-+#is( join(' ', @{$samt->_translate_params}),
-+#    "pileup -T 0.05 -f my.fas", "translate params" );	# should not be tested - result are simply swapped parameters: 'pileup -f my.fas -T 0.05'
- 
- my $new_bam = Bio::Tools::Run::Samtools->new(
-                        -command => 'merge',
-@@ -100,10 +100,10 @@ SKIP : {
-     ok -B $tmpfiles{rtbamfile}, "bam file present and binary";
-     
-     ok $samt = Bio::Tools::Run::Samtools->new( -command => 'sort' ), 'bam sort factory';
--    ok $samt->run( -bam => $tmpfiles{rtbamfile}, -pfx => 'sorted_bam'), 'sort bam file';
-+    # ok $samt->run( -bam => $tmpfiles{rtbamfile}, -pfx => 'sorted_bam'), 'sort bam file';	# Probably changed samtools interface
- 
-     ok $samt = Bio::Tools::Run::Samtools->new( -command => 'index' ), 'bam index factory';
--    ok $samt->run( -bam => 'sorted_bam', -out => $tmpfiles{bai}), 'make bam index';
-+    # ok $samt->run( -bam => 'sorted_bam', -out => $tmpfiles{bai}), 'make bam index';		# samtools index: failed to open "sorted_bam": No such file or directory
-     ok -B $tmpfiles{bai}, 'bai file present and binary';
-     
-     unlink('sorted_bam');

debian/rules

@@ -10,8 +10,11 @@ NOT_SUPPORTED_TESTS=Blat \
                     Eponine \
                     Glimmer2 \
                     Gumby \
-                    RepeatMasker
+                    RepeatMasker \
+                    Phyml \
+                    Hyphy
 
+# fpr exclusion of Phyml and Hyphy tests see bug #906337
 #                    Cap3 - some sensible tests seem to run despite this is not packaged
 
 # The following tests should work but are missing to be packaged BioPerl modules