[med-svn] [Git][med-team/ariba][master] 5 commits: suggest SPAdes

Sascha Steinbiss gitlab at salsa.debian.org
Tue Jun 30 11:45:13 BST 2020 


Sascha Steinbiss pushed to branch master at Debian Med / ariba


Commits:
7f99111f by Sascha Steinbiss at 2020-06-30T12:36:27+02:00
suggest SPAdes

- - - - -
f1f2bff2 by Sascha Steinbiss at 2020-06-30T12:37:16+02:00
add patch to fix test failures

- - - - -
b5606c2d by Sascha Steinbiss at 2020-06-30T12:37:29+02:00
add patch to call SPAdes correctly

- - - - -
6f7ba395 by Sascha Steinbiss at 2020-06-30T12:37:43+02:00
add upstream metadata

- - - - -
f5f3d044 by Sascha Steinbiss at 2020-06-30T12:37:54+02:00
use debhelper 13

- - - - -


6 changed files:

- debian/changelog
- debian/control
- + debian/patches/run-debian-spades-wrapper.patch
- debian/patches/series
- + debian/patches/support-pymummer-0.11.patch
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,10 +1,17 @@
-ariba (2.14.5+ds-2) UNRELEASED; urgency=medium
+ariba (2.14.5+ds-2) unstable; urgency=medium
 
-  * Team upload.
+  [ Andreas Tille ]
   * Build-Depends: spades <!nocheck>
-  * Depends: spades
+  * Suggests: spades
+
+  [ Sascha Steinbiss ]
+  * Add patch to fix test failures.
+    Closes: #963332
+  * Add patch to call SPAdes correctly.
+  * Add upstream metadata.
+  * Use debhelper 13.
 
- -- Andreas Tille <tille at debian.org>  Mon, 22 Jun 2020 11:29:55 +0200
+ -- Sascha Steinbiss <satta at debian.org>  Tue, 30 Jun 2020 12:32:39 +0200
 
 ariba (2.14.5+ds-1) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Sascha Steinbiss <satta at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
                dh-python,
                python3-biopython,
                python3-all-dev,
@@ -47,8 +47,8 @@ Depends: ${misc:Depends},
          python3-pysam (>= 0.9.1),
          python3-matplotlib,
          python3-tk,
-         fastaq (>= 3.12.0),
-         spades
+         fastaq (>= 3.12.0)
+Suggests: spades
 Description: Antibiotic Resistance Identification By Assembly
  ARIBA is a tool that identifies antibiotic resistance genes by running local
  assemblies.


=====================================
debian/patches/run-debian-spades-wrapper.patch
=====================================
@@ -0,0 +1,19 @@
+Description: run Debian SPAdes wrapper
+ Debian's /usr/bin/spades.py is not a Python script, but a wrapper
+ around a common executable only provided for compatibility reasons.
+ Ariba is trying to execute it explicitly as a Python script.
+ This patch just calls the executable without forcing it through the
+ Python interpreter.
+Author: Sascha Steinbiss <satta at debian.org>
+Last-Update: 2020-06-30
+--- a/ariba/assembly.py
++++ b/ariba/assembly.py
+@@ -140,7 +140,7 @@
+                 spades_out_seq_base = "contigs.fasta"
+             else:
+                 raise ValueError("Unknown spades_mode value: {}".format(self.spades_mode))
+-            asm_cmd = ['python3', spades_exe, "-t", str(self.threads), "--pe1-1", self.reads1, "--pe1-2", self.reads2, "-o", self.assembler_dir] + \
++            asm_cmd = [spades_exe, "-t", str(self.threads), "--pe1-1", self.reads1, "--pe1-2", self.reads2, "-o", self.assembler_dir] + \
+                 spades_options
+             asm_ok,err = common.syscall(asm_cmd, verbose=True, verbose_filehandle=self.log_fh, shell=False, allow_fail=True)
+             if not asm_ok:


=====================================
debian/patches/series
=====================================
@@ -2,3 +2,5 @@ use_debian_packaged_libs_for_extension.patch
 use_bwa_compatible_fermi-lite.patch
 add-testdata.patch
 disable-tests-with-internet-access.patch
+support-pymummer-0.11.patch
+run-debian-spades-wrapper.patch


=====================================
debian/patches/support-pymummer-0.11.patch
=====================================
@@ -0,0 +1,176 @@
+Description: adapt test cases for new PyMUMmer version
+ pymummer 0.11 uses a different internal format which is incompatible
+ with the one assumed by Ariba. Note that ariba hard-requires an earlier
+ version than the one in Debian. However, since Debian has updated
+ pymummer now, we need to catch up even though upstream does not.
+Author: Sascha Steinbiss <satta at debian.org>
+Last-Update: 2020-06-30
+--- a/ariba/tests/assembly_variants_test.py
++++ b/ariba/tests/assembly_variants_test.py
+@@ -52,23 +52,23 @@
+     def test_get_variant_effect(self):
+         '''test _get_variant_effect'''
+         ref_seq = pyfastaq.sequences.Fasta('gene', 'GATCGCGAAGCGATGACCCATGAAGCGACCGAACGCTGA')
+-        v1 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tT\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
+-        v1 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tT\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
+-        v2 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tA\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
+-        v3 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tT\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
+-        v4 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tA\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
+-        v5 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\t.\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
+-        v6 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tA\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
+-        v7 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tG\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
++        v1 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tT\t6\tx\tx\t39\t39\tx\t1\tgene\tcontig'))
++        v1 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tT\t6\tx\tx\t39\t39\tx\t1\tgene\tcontig'))
++        v2 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tA\t6\tx\tx\t39\t39\tx\t1\tgene\tcontig'))
++        v3 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tT\t4\tx\tx\t39\t39\tx\t1\tgene\tcontig'))
++        v4 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tA\t6\tx\tx\t39\t39\tx\t1\tgene\tcontig'))
++        v5 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\t.\t4\tx\tx\t39\t39\tx\t1\tgene\tcontig'))
++        v6 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tA\t4\tx\tx\t39\t39\tx\t1\tgene\tcontig'))
++        v7 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tG\t4\tx\tx\t39\t39\tx\t1\tgene\tcontig'))
+         v7.qry_base = 'GAT'
+-        v8 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tG\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
++        v8 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tG\t4\tx\tx\t39\t39\tx\t1\tgene\tcontig'))
+         v8.qry_base = 'TGA'
+-        v9 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tG\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
++        v9 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tG\t4\tx\tx\t39\t39\tx\t1\tgene\tcontig'))
+         v9.qry_base = 'ATTCCT'
+-        v10 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\t.\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
++        v10 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\t.\t4\tx\tx\t39\t39\tx\t1\tgene\tcontig'))
+         v10.ref_base = 'CGC'
+         v10.ref_end = 5
+-        v11 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\t.\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
++        v11 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\t.\t4\tx\tx\t39\t39\tx\t1\tgene\tcontig'))
+         v11.ref_base = 'CGCGAA'
+         v11.ref_end = 8
+ 
+@@ -93,9 +93,9 @@
+     def test_filter_mummer_variants(self):
+         '''test filter_mummer_variants'''
+         ref_seq = pyfastaq.sequences.Fasta('gene', 'GATCGCGAAGCGATGACCCATGAAGCGACCGAACGCTGA')
+-        v1 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tT\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
+-        v2 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tA\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
+-        v3 = pymummer.variant.Variant(pymummer.snp.Snp('12\tG\tT\t12\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
++        v1 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tT\t4\tx\tx\t39\t39\tx\t1\tgene\tcontig'))
++        v2 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tA\t6\tx\tx\t39\t39\tx\t1\tgene\tcontig'))
++        v3 = pymummer.variant.Variant(pymummer.snp.Snp('12\tG\tT\t12\tx\tx\t39\t39\tx\t1\tgene\tcontig'))
+         mummer_variants = {'contig': [[v1, v2], v3]}
+         assembly_variants.AssemblyVariants._filter_mummer_variants(mummer_variants, ref_seq)
+         expected = {'contig': [[v1, v2]]}
+@@ -110,13 +110,13 @@
+         ref_sequence_name = 'non_coding'
+         refdata_var_dict = refdata.metadata[ref_sequence_name]
+ 
+-        v0 = pymummer.variant.Variant(pymummer.snp.Snp('2\tT\tA\t2\tx\tx\t42\t42\tx\tx\tnon_coding\tcontig'))
++        v0 = pymummer.variant.Variant(pymummer.snp.Snp('2\tT\tA\t2\tx\tx\t42\t42\tx\t1\tnon_coding\tcontig'))
+ 
+         # ref has A at position 3, which is variant type. This gives contig the wild type C. Shouldn't report
+-        v1 = pymummer.variant.Variant(pymummer.snp.Snp('3\tA\tC\t3\tx\tx\t42\t42\tx\tx\tnon_coding\tcontig'))
++        v1 = pymummer.variant.Variant(pymummer.snp.Snp('3\tA\tC\t3\tx\tx\t42\t42\tx\t1\tnon_coding\tcontig'))
+ 
+         # ref has T at position 5, which is wild type. This gives contig variant type A. Should report
+-        v2 = pymummer.variant.Variant(pymummer.snp.Snp('5\tT\tA\t5\tx\tx\t42\t42\tx\tx\tnon_coding\tcontig'))
++        v2 = pymummer.variant.Variant(pymummer.snp.Snp('5\tT\tA\t5\tx\tx\t42\t42\tx\t1\tnon_coding\tcontig'))
+ 
+         meta0 = sequence_metadata.SequenceMetadata('non_coding\t0\t0\tC3A\tid1\tref has variant type A')
+         meta2 = sequence_metadata.SequenceMetadata('non_coding\t0\t0\tT5A\tid1\tref has wild type T')
+@@ -153,33 +153,33 @@
+         ref_sequence = refdata.sequence(ref_sequence_name)
+         refdata_var_dict = refdata.metadata[ref_sequence_name]
+ 
+-        v0 = pymummer.variant.Variant(pymummer.snp.Snp('6\tT\tA\t6\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
+-        v1 = pymummer.variant.Variant(pymummer.snp.Snp('9\tA\tT\t9\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
+-        v2 = pymummer.variant.Variant(pymummer.snp.Snp('18\tG\tT\t18\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
+-        v3 = pymummer.variant.Variant(pymummer.snp.Snp('21\tC\tT\t21\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
+-        v4 = pymummer.variant.Variant(pymummer.snp.Snp('7\tA\tT\t7\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
+-        v5 = pymummer.variant.Variant(pymummer.snp.Snp('12\tA\tC\t11\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
+-
+-        v6 = pymummer.variant.Variant(pymummer.snp.Snp('4\tG\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
+-        self.assertTrue(v6.update_indel(pymummer.snp.Snp('5\tA\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
+-
+-        v7 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tA\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
+-        self.assertTrue(v7.update_indel(pymummer.snp.Snp('4\t.\tA\t5\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
+-
+-        v8 = pymummer.variant.Variant(pymummer.snp.Snp('4\tG\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
+-        self.assertTrue(v8.update_indel(pymummer.snp.Snp('5\tA\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
+-        self.assertTrue(v8.update_indel(pymummer.snp.Snp('6\tT\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
+-
+-        v9 = pymummer.variant.Variant(pymummer.snp.Snp('4\tG\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
+-        self.assertTrue(v9.update_indel(pymummer.snp.Snp('5\tA\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
+-        self.assertTrue(v9.update_indel(pymummer.snp.Snp('6\tT\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
+-        self.assertTrue(v9.update_indel(pymummer.snp.Snp('7\tA\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
+-        self.assertTrue(v9.update_indel(pymummer.snp.Snp('8\tG\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
+-        self.assertTrue(v9.update_indel(pymummer.snp.Snp('9\tA\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
+-
+-        v10 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tA\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
+-        self.assertTrue(v10.update_indel(pymummer.snp.Snp('4\t.\tT\t5\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
+-        self.assertTrue(v10.update_indel(pymummer.snp.Snp('4\t.\tT\t6\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
++        v0 = pymummer.variant.Variant(pymummer.snp.Snp('6\tT\tA\t6\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))
++        v1 = pymummer.variant.Variant(pymummer.snp.Snp('9\tA\tT\t9\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))
++        v2 = pymummer.variant.Variant(pymummer.snp.Snp('18\tG\tT\t18\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))
++        v3 = pymummer.variant.Variant(pymummer.snp.Snp('21\tC\tT\t21\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))
++        v4 = pymummer.variant.Variant(pymummer.snp.Snp('7\tA\tT\t7\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))
++        v5 = pymummer.variant.Variant(pymummer.snp.Snp('12\tA\tC\t11\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))
++
++        v6 = pymummer.variant.Variant(pymummer.snp.Snp('4\tG\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))
++        self.assertTrue(v6.update_indel(pymummer.snp.Snp('5\tA\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))
++
++        v7 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tA\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))
++        self.assertTrue(v7.update_indel(pymummer.snp.Snp('4\t.\tA\t5\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))
++
++        v8 = pymummer.variant.Variant(pymummer.snp.Snp('4\tG\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))
++        self.assertTrue(v8.update_indel(pymummer.snp.Snp('5\tA\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))
++        self.assertTrue(v8.update_indel(pymummer.snp.Snp('6\tT\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))
++
++        v9 = pymummer.variant.Variant(pymummer.snp.Snp('4\tG\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))
++        self.assertTrue(v9.update_indel(pymummer.snp.Snp('5\tA\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))
++        self.assertTrue(v9.update_indel(pymummer.snp.Snp('6\tT\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))
++        self.assertTrue(v9.update_indel(pymummer.snp.Snp('7\tA\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))
++        self.assertTrue(v9.update_indel(pymummer.snp.Snp('8\tG\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))
++        self.assertTrue(v9.update_indel(pymummer.snp.Snp('9\tA\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))
++
++        v10 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tA\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))
++        self.assertTrue(v10.update_indel(pymummer.snp.Snp('4\t.\tT\t5\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))
++        self.assertTrue(v10.update_indel(pymummer.snp.Snp('4\t.\tT\t6\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))
+ 
+         mummer_variants = [[v0], [v1], [v2], [v3], [v4], [v5], [v6], [v7], [v8], [v9], [v10]]
+ 
+@@ -306,8 +306,8 @@
+         os.unlink(metadata_tsv)
+ 
+         nucmer_snp_file = os.path.join(data_dir, 'assembly_variants_test_get_variants_presence_absence.snps')
+-        v2 = pymummer.variant.Variant(pymummer.snp.Snp('14\tC\tA\t14\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig1'))
+-        v3 = pymummer.variant.Variant(pymummer.snp.Snp('15\tG\tC\t15\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig1'))
++        v2 = pymummer.variant.Variant(pymummer.snp.Snp('14\tC\tA\t14\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig1'))
++        v3 = pymummer.variant.Variant(pymummer.snp.Snp('15\tG\tC\t15\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig1'))
+ 
+         ref_nucmer_coords = {
+             'contig1': [pyfastaq.intervals.Interval(0, 30)],
+@@ -354,8 +354,8 @@
+         os.unlink(metadata_tsv)
+ 
+         nucmer_snp_file = os.path.join(data_dir, 'assembly_variants_test_get_variants_variants_only.snps')
+-        v2 = pymummer.variant.Variant(pymummer.snp.Snp('14\tC\tA\t14\tx\tx\t42\t42\tx\tx\tvariants_only\tcontig1'))
+-        v3 = pymummer.variant.Variant(pymummer.snp.Snp('15\tG\tC\t15\tx\tx\t42\t42\tx\tx\tvariants_only\tcontig1'))
++        v2 = pymummer.variant.Variant(pymummer.snp.Snp('14\tC\tA\t14\tx\tx\t42\t42\tx\t1\tvariants_only\tcontig1'))
++        v3 = pymummer.variant.Variant(pymummer.snp.Snp('15\tG\tC\t15\tx\tx\t42\t42\tx\t1\tvariants_only\tcontig1'))
+ 
+         ctg_nucmer_coords = {
+             'contig1': [pyfastaq.intervals.Interval(0, 41)],
+--- a/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps
++++ b/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps
+@@ -1,3 +1,3 @@
+-9	A	T	9	x	x	42	42	x	x	variants_only	contig1
+-14	C	A	14	x	x	42	42	x	x	variants_only	contig1
+-15	G	C	15	x	x	42	42	x	x	variants_only	contig1
++9	A	T	9	x	x	42	42	x	1	variants_only	contig1
++14	C	A	14	x	x	42	42	x	1	variants_only	contig1
++15	G	C	15	x	x	42	42	x	1	variants_only	contig1
+--- a/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps
++++ b/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps
+@@ -1,3 +1,3 @@
+-9	A	T	9	x	x	42	42	x	x	presence_absence	contig1
+-14	C	A	14	x	x	42	42	x	x	presence_absence	contig1
+-15	G	C	15	x	x	42	42	x	x	presence_absence	contig1
++9	A	T	9	x	x	42	42	x	1	presence_absence	contig1
++14	C	A	14	x	x	42	42	x	1	presence_absence	contig1
++15	G	C	15	x	x	42	42	x	1	presence_absence	contig1


=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,7 @@
+Bug-Database: https://github.com/sanger-pathogens/ariba
+Bug-Submit: https://github.com/sanger-pathogens/ariba/issues/new
+Repository: https://github.com/sanger-pathogens/ariba.git
+Repository-Browse: https://github.com/sanger-pathogens/ariba
 Reference:
  - Author: >
     Martin Hunt and Alison E. Mather and Leonor Sanchez-Buso and Andrew



View it on GitLab: https://salsa.debian.org/med-team/ariba/-/compare/fba3b82104d2b898e68321aacd0826328058006b...f5f3d044d5a992aa730445a0f6077462fc0b0b83

-- 
View it on GitLab: https://salsa.debian.org/med-team/ariba/-/compare/fba3b82104d2b898e68321aacd0826328058006b...f5f3d044d5a992aa730445a0f6077462fc0b0b83
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