--- 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"