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bigwigcat container is missing dependency #335

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nsheff opened this issue Aug 2, 2019 · 3 comments
Open

bigwigcat container is missing dependency #335

nsheff opened this issue Aug 2, 2019 · 3 comments

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@nsheff
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nsheff commented Aug 2, 2019

The latest ucsc-bigwigcat container is missing a shared object:

>   quay.io/biocontainers/ucsc-bigwigcat:377--h199ee4e_0 bigWigCat

bigWigCat: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory

The older container appears to work:

docker run --rm \
>   quay.io/biocontainers/ucsc-bigwigcat:357--1 bigWigCat
bigWigCat v 4 - merge non-overlapping bigWig files
directly into bigWig format
usage:
   bigWigCat out.bw in1.bw in2.bw ...
Where in*.bw is in big wig format
and out.bw is the output indexed big wig file.
options:
   -itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024

Note: must use wigToBigWig -fixedSummaries -keepAllChromosomes (perhaps in parallel cluster jobs) to create the input files.
Note: By non-overlapping we mean the entire span of each file, from first data point to last data point, must not overlap with that of other files.
@osallou
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osallou commented Aug 2, 2019

This should be fixed in bioconda package, could you open issue there?

@nsheff
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nsheff commented Jun 29, 2020

can you be more specific about where "there" is, exactly?

@osallou
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osallou commented Jun 29, 2020

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