Merge pull request #15 from broadinstitute/dp-refbased

viral-core 2.1.4
broadinstitute · Jun 20, 2020 · 2289f5d · 2289f5d
2 parents 907d347 + c79d064
commit 2289f5d
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Showing 3 changed files with 8 additions and 8 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM quay.io/broadinstitute/viral-core:2.1.3
+FROM quay.io/broadinstitute/viral-core:2.1.4
 
 LABEL maintainer "[email protected]"
 

diff --git a/requirements-conda.txt b/requirements-conda.txt
@@ -1,7 +1,7 @@
-gap2seq=3.1.1a2
-mafft=7.464
-mummer4=4.0.0beta2
-muscle=3.8.1551 
-spades=3.12.0
+gap2seq>=3.1.1a2
+mafft>=7.464
+mummer4>=4.0.0beta2
+muscle>=3.8.1551
+spades>=3.12.0
 trinity=date.2011_11_26
 # Python packages below
diff --git a/test/unit/test_assembly.py b/test/unit/test_assembly.py
@@ -159,7 +159,7 @@ def test_assembly(self):
             contig_lens = list(sorted(len(seq.seq) for seq in Bio.SeqIO.parse(outFasta, 'fasta')))
             #import sys
             #print('test_assembly_contigs_lens:', contig_lens, file=sys.stderr)
-            self.assertEqual(contig_lens, [180, 184, 187, 190, 191, 194, 197, 211, 243, 244, 247, 288, 328, 348, 430])
+            self.assertEqual(contig_lens, [190, 195, 197, 222, 243, 247, 359])
 
     def test_assembly_with_previously_assembled_contigs(self):
         inDir = util.file.get_test_input_path(self)
@@ -173,7 +173,7 @@ def test_assembly_with_previously_assembled_contigs(self):
             contig_lens = list(sorted(len(seq.seq) for seq in Bio.SeqIO.parse(outFasta, 'fasta')))
             #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])
+            self.assertEqual(contig_lens, [172, 174, 190, 195, 197, 222, 243, 247, 359])
 
     def test_empty_input_succeed(self):
         inDir = util.file.get_test_input_path()