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maxbin2: add idba out/err only if present (and update bioconda recipe)#2706

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bgruening merged 2 commits intogalaxyproject:masterfrom
bernt-matthias:topic/maxbin2-container-fixes
Dec 1, 2019
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maxbin2: add idba out/err only if present (and update bioconda recipe)#2706
bgruening merged 2 commits intogalaxyproject:masterfrom
bernt-matthias:topic/maxbin2-container-fixes

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@bernt-matthias
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  • replaced by gzip -cd | tar -xf -
  • additionally add idba out/err only if present

FOR CONTRIBUTOR:

  • - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • - License permits unrestricted use (educational + commercial)
  • - This PR adds a new tool or tool collection
  • - This PR updates an existing tool or tool collection
  • - This PR does something else (explain below)

- replaced by `gzip -cd | tar -xf -`
- additionally add idba out/err only if present
@bernt-matthias
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bump?

@bgruening
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Think so yes! please bump.

@mvdbeek
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mvdbeek commented Nov 30, 2019

This is still failing in the container with:


Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

tar: invalid option -- 'z'
BusyBox v1.22.1 (2014-05-23 01:24:27 UTC) multi-call binary.

Usage: tar -[cxthvO] [-X FILE] [-T FILE] [-f TARFILE] [-C DIR] [FILE]...

Create, extract, or list files from a tar file

Operation:
	c	Create
	x	Extract
	t	List
	f	Name of TARFILE ('-' for stdin/out)
	C	Change to DIR before operation
	v	Verbose
	O	Extract to stdout
	h	Follow symlinks
	exclude	File to exclude
	X	File with names to exclude
	T	File with names to include

gzip: out.marker_of_each_bin.tar.gz: No such file or directory
tar: short read

I think maxbin2 might be using tar internally ? In which case we should add a dependency on https://anaconda.org/conda-forge/tar ... probably to the bioconda package ?

@bernt-matthias
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Awesome, thanks @bernt-matthias !

@mvdbeek mvdbeek changed the title maxbin2: omit tar decompression option maxbin2: add idba out/err only if present (and update bioconda recipe) Dec 1, 2019
@bgruening bgruening merged commit fe30b00 into galaxyproject:master Dec 1, 2019
@bernt-matthias bernt-matthias deleted the topic/maxbin2-container-fixes branch March 8, 2020 10:38
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3 participants