bcbio is on salsa - builds .debs, importable from python, missig seqcluster (at least) and python(2)-toolz

[Steffen Möller <steffen_moeller@gmx.de>]

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.