Hello, The subject line says it all. I am admittedly somewhat happy about that, but I was cheating:
- pybedtools would need to resurface in the distro but its tests fail beyond my comprehension - cyvcf2 is in a new version 0.9.0 now, but, well, tests fail. It comes with its own version of htslib, which may well contribute to the situation since I had nothing better to do than to substitute it with the one the distribution ships. Is anybody close to upstream on this list to have a look? - bcbio's tests run into some issue that has been reported to be a panda issue - shown below. The libraries required to run bcbio are yet incomplete. The latest I got across ist seqcluster and for python2 there is no toolz library :o/ Without toolz the scripts are not executable. And in python3 one runs quickly into a syntax error. So, I think we need to decide if we want bcbio with us. My answer is "yes", still. But this would need some work on pybedtools and cyvcf2. I just saw that Diane packaged toolz just recently. @Diane, if you read this, do you mind me extending this for python2? Best, Steffen ERROR: bcbio.workflow (unittest.loader._FailedTest) ---------------------------------------------------------------------- ImportError: Failed to import test module: bcbio.workflow Traceback (most recent call last): File "/usr/lib/python3/dist-packages/pandas/__init__.py", line 26, in <module> from pandas._libs import (hashtable as _hashtable, File "/usr/lib/python3/dist-packages/pandas/_libs/__init__.py", line 4, in <module> from .tslib import iNaT, NaT, Timestamp, Timedelta, OutOfBoundsDatetime ModuleNotFoundError: No module named 'pandas._libs.tslib' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3.7/unittest/loader.py", line 468, in _find_test_path package = self._get_module_from_name(name) File "/usr/lib/python3.7/unittest/loader.py", line 375, in _get_module_from_name __import__(name) File "/home/moeller/git/debian-med/bcbio/.pybuild/cpython3_3.7_bcbio/build/bcbio/workflow/__init__.py", line 3, in <module> from bcbio.workflow import xprize, stormseq, template File "/home/moeller/git/debian-med/bcbio/.pybuild/cpython3_3.7_bcbio/build/bcbio/workflow/stormseq.py", line 11, in <module> from bcbio.upload import s3 File "/home/moeller/git/debian-med/bcbio/.pybuild/cpython3_3.7_bcbio/build/bcbio/upload/__init__.py", line 9, in <module> from bcbio.upload import shared, filesystem, galaxy, s3, irods File "/home/moeller/git/debian-med/bcbio/.pybuild/cpython3_3.7_bcbio/build/bcbio/upload/galaxy.py", line 15, in <module> from bcbio.pipeline import qcsummary File "/home/moeller/git/debian-med/bcbio/.pybuild/cpython3_3.7_bcbio/build/bcbio/pipeline/qcsummary.py", line 16, in <module> from bcbio.pipeline import config_utils, run_info File "/home/moeller/git/debian-med/bcbio/.pybuild/cpython3_3.7_bcbio/build/bcbio/pipeline/run_info.py", line 17, in <module> from bcbio import install, utils, structural File "/home/moeller/git/debian-med/bcbio/.pybuild/cpython3_3.7_bcbio/build/bcbio/structural/__init__.py", line 13, in <module> from bcbio.structural import (battenberg, cn_mops, cnvkit, delly, gridss, File "/home/moeller/git/debian-med/bcbio/.pybuild/cpython3_3.7_bcbio/build/bcbio/structural/cnvkit.py", line 28, in <module> from bcbio.structural import annotate, plot, shared File "/home/moeller/git/debian-med/bcbio/.pybuild/cpython3_3.7_bcbio/build/bcbio/structural/plot.py", line 12, in <module> from bcbio.bam.coverage import plot_multiple_regions_coverage File "/home/moeller/git/debian-med/bcbio/.pybuild/cpython3_3.7_bcbio/build/bcbio/bam/coverage.py", line 7, in <module> import pandas as pd File "/usr/lib/python3/dist-packages/pandas/__init__.py", line 35, in <module> "the C extensions first.".format(module)) ImportError: C extension: No module named 'pandas._libs.tslib' not built. If you want to import pandas from the source directory, you may need to run 'python setup.py build_ext --inplace --force' to build the C extensions first.
