Re: bcbio is on salsa - builds .debs, importable from python, missig seqcluster (at least) and python(2)-toolz
Hi,
Steffen, if you think Liubov might be able to help at getting tests
working it is fine for me if she wants to tackle this. Possibly some
Python3 porting work might make the package more future proof - no
idea how much work this might mean.
@Steffen: May be to get Liubov started its helpful if you provide some
more verbose information with links.
Kind regards
Andreas.
On Sun, Jul 08, 2018 at 12:23:08AM +0200, Steffen Möller wrote:
> 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.
>
>
>
--
http://fam-tille.de
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