From e8da5165a38e9a829788a6e52af07d06011e6769 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Sat, 20 Jun 2020 11:03:45 -0400 Subject: [PATCH 1/4] bump viral-core --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 81f1e270..b3e7471f 100644 --- 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 "viral-ngs@broadinstitute.org" From 3956d4cef63b12b6ce458e0b77a7f5550075bcad Mon Sep 17 00:00:00 2001 From: Danny Park Date: Sat, 20 Jun 2020 11:16:16 -0400 Subject: [PATCH 2/4] flex pinned versions of conda packages --- requirements-conda.txt | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/requirements-conda.txt b/requirements-conda.txt index 1682fc7a..aa829b2c 100644 --- 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 From 9edde176801694d6b11854fe58aa1f197dd77769 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Sat, 20 Jun 2020 11:16:51 -0400 Subject: [PATCH 3/4] del trailing space --- requirements-conda.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements-conda.txt b/requirements-conda.txt index aa829b2c..67e64f14 100644 --- 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 +muscle>=3.8.1551 spades>=3.12.0 trinity=date.2011_11_26 # Python packages below From c79d06429bd9c22a64142b0df35ba0c083c1bf6b Mon Sep 17 00:00:00 2001 From: Danny Park Date: Sat, 20 Jun 2020 11:41:26 -0400 Subject: [PATCH 4/4] update expected contig lengths in unit tests --- test/unit/test_assembly.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/unit/test_assembly.py b/test/unit/test_assembly.py index 7a25cbd3..31f55210 100644 --- 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()