diff options
Diffstat (limited to 'sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch')
| -rw-r--r-- | sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch | 37 |
1 files changed, 37 insertions, 0 deletions
diff --git a/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch b/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch new file mode 100644 index 000000000000..9d269878e651 --- /dev/null +++ b/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch @@ -0,0 +1,37 @@ +--- a/tests/pysam_data/Makefile ++++ b/tests/pysam_data/Makefile +@@ -3,7 +3,7 @@ + BAI=$(BAM:%.bam=%.bam.bai) + CRAM=ex1.cram ex2.cram ex3.cram + CRAI=$(CRAM:%.cram=%.cram.crai) +-NO_PG:=$(findstring --no-PG,$(shell samtools view)) ++NO_PG:=--no-PG + + # ex2.bam - bam file without index + +--- a/tests/tabix_test.py ++++ b/tests/tabix_test.py +@@ -14,6 +14,7 @@ + import subprocess + import glob + import re ++import pytest + from TestUtils import checkBinaryEqual, checkGZBinaryEqual, check_url, \ + load_and_convert, TABIX_DATADIR, get_temp_filename + +@@ -1014,6 +1015,7 @@ + globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,)) + + ++@pytest.mark.skip(reason="requires internet connectivity") + class TestRemoteFileHTTP(unittest.TestCase): + + url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz" +@@ -1053,6 +1055,7 @@ + self.assertEqual(list(self.local_file.header), []) + + ++@pytest.mark.skip(reason="requires internet connectivity") + class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP): + + url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz" |