[Debian-med-packaging] Bug#980005: lumpy-sv: lumpyexpress fails with no args

[Andreas Tille]

Control: tags -1 confirmed
Control: tags -1 help

Hi,

I confirm I can reproduce the issue in a minimal chroot while the
lumpyexpress command prints the help screen as expected.  This smells
like a missing dependency but I do not have any idea which one.  It
seems there is a similar known issue here

   https://stackoverflow.com/questions/65028261/attributeerror-module-importlib-has-no-attribute-util-ii

but there is no answer here.

Any idea how to fix this?

Kind regards

      Andreas.

On Tue, Jan 12, 2021 at 08:05:26PM +0000, Ken Yamaguchi wrote:
> Package: lumpy-sv
> Version: 0.3.1+dfsg-4
> Severity: important
> X-Debbugs-Cc: debian at knowledgesynthesis.com
> 
> Dear Maintainer,
> 
> I built a lumpy-sv Docker image with the attached Dockerfile. Running a container for the image produces the following error:
> 
> Sourcing executables from /etc/lumpy-sv/lumpyexpress.config ...
> 
> Checking for required python modules (/usr/bin/python3)...
> Traceback (most recent call last):
>   File "<string>", line 1, in <module>
> AttributeError: module 'importlib' has no attribute 'util'
> 
> Thanks,
> Ken
> 
> -- System Information:
> Debian Release: bullseye/sid
>   APT prefers testing
>   APT policy: (500, 'testing')
> Architecture: amd64 (x86_64)
> 
> Kernel: Linux 4.19.0-13-amd64 (SMP w/4 CPU threads)
> Kernel taint flags: TAINT_WARN
> Locale: LANG=C, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE not set
> Shell: /bin/sh linked to /bin/dash
> Init: unable to detect
> 
> Versions of packages lumpy-sv depends on:
> ii  bamkit            0.0.1+git20170413.ccd079d-2
> ii  libbamtools2.5.1  2.5.1+dfsg-7+b1
> ii  libc6             2.31-9
> ii  libgcc-s1         10.2.1-3
> ii  libgzstream0      1.5+dfsg-5
> ii  libhts3           1.11-4
> ii  libstdc++6        10.2.1-3
> ii  python3           3.9.1-1
> ii  python3-numpy     1:1.19.4-1+b1
> ii  python3-pysam     0.15.4+ds-3+b2
> ii  samblaster        0.1.26-1
> ii  samtools          1.11-1
> 
> Versions of packages lumpy-sv recommends:
> pn  sambamba  <none>
> 
> lumpy-sv suggests no packages.
> 
> -- no debconf information

> FROM debian:bullseye-slim
> 
> RUN apt-get update && \
>     apt-get -y --no-install-recommends full-upgrade && \
>     apt-get -y --no-install-recommends install \
>         lumpy-sv \
>         && \
>     rm -rf /var/lib/apt/lists/*
> 
> RUN useradd -ms /bin/bash lumpy
> 
> USER lumpy
> 
> WORKDIR /home/lumpy
> 
> CMD ["lumpyexpress"]

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