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, 0 insertions, 37 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 deleted file mode 100644 index 9d269878e651..000000000000 --- a/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch +++ /dev/null @@ -1,37 +0,0 @@ ---- 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" |