Merge branch 'master' into is-bump-coveralls-to-1.3

broadinstitute · Aug 14, 2018 · 1247bc6 · 1247bc6
2 parents 0316326 + 0931224
commit 1247bc6
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Showing 3 changed files with 8 additions and 6 deletions.
diff --git a/requirements-conda.txt b/requirements-conda.txt
@@ -23,7 +23,7 @@ pigz=2.4
 prinseq=0.20.4
 samtools=1.9
 snpeff=4.3.1t
-spades=3.11.1
+spades=3.12.0
 tbl2asn=25.6
 trimmomatic=0.38
 trinity=date.2011_11_26

diff --git a/test/unit/test_assembly.py b/test/unit/test_assembly.py
@@ -157,8 +157,9 @@ def test_assembly(self):
             assembly.assemble_spades(in_bam=inBam, clip_db=clipDb, out_fasta=outFasta)
             self.assertGreater(os.path.getsize(outFasta), 0)
             contig_lens = list(sorted(len(seq.seq) for seq in Bio.SeqIO.parse(outFasta, 'fasta')))
-            print('test_assembly_contigs_lens:', contig_lens)
-            self.assertEqual(contig_lens, [168, 170, 177, 180, 184, 187, 190, 191, 195, 197, 211, 243, 244, 247, 328, 348, 430])
+            #import sys
+            #print('test_assembly_contigs_lens:', contig_lens, file=sys.stderr)
+            self.assertEqual(contig_lens, [168, 170, 177, 180, 184, 187, 190, 191, 194, 197, 211, 243, 244, 247, 288, 328, 348, 430])
 
     def test_assembly_with_previously_assembled_contigs(self):
         inDir = util.file.get_test_input_path(self)
@@ -170,8 +171,9 @@ def test_assembly_with_previously_assembled_contigs(self):
                                      out_fasta=outFasta, mem_limit_gb=1)
             self.assertGreater(os.path.getsize(outFasta), 0)
             contig_lens = list(sorted(len(seq.seq) for seq in Bio.SeqIO.parse(outFasta, 'fasta')))
-            print('test_assembly_with_previously_assembled_contigs_contigs_lens:', contig_lens)
-            self.assertEqual(contig_lens, [168, 170, 177, 180, 184, 187, 190, 191, 195, 197, 211, 243, 244, 321, 328, 348, 430])
+            #import sys
+            #print('test_assembly_with_previously_assembled_contigs_contigs_lens:', contig_lens, file=sys.stderr)
+            self.assertEqual(contig_lens, [168, 170, 177, 180, 184, 187, 190, 191, 194, 197, 211, 243, 244, 247, 288, 328, 348, 430])
 
     def test_empty_input_succeed(self):
         inDir = util.file.get_test_input_path()

diff --git a/tools/spades.py b/tools/spades.py
@@ -18,7 +18,7 @@
 import util.misc
 
 TOOL_NAME = 'spades'
-TOOL_VERSION = '3.11.1'
+TOOL_VERSION = '3.12.0'
 
 log = logging.getLogger(__name__)