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bigwigcat container is missing dependency

Open nsheff opened this issue 6 years ago • 3 comments

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.

nsheff avatar Aug 02 '19 11:08 nsheff

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

osallou avatar Aug 02 '19 12:08 osallou

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

nsheff avatar Jun 29 '20 17:06 nsheff

https://github.com/bioconda/bioconda-recipes

osallou avatar Jun 29 '20 20:06 osallou