Hi Folks,

I'm still having difficulty with this...just wondering if anyone has seen
this before:

For some reason, I only had one time success with installing dexseq 1.22 in
the docker galaxy, which I didn't know how it worked
out. After that, when I run biocLite("DEXSeq") again, it only installs
dexseq 1.20, or even older version. I think this has something
to do with R version and bioconductor version. However, R in the conda-env
doesn't run -- it has some dependency libraries missing
seems, libicui18n etc and I could not easily resolve that. :-(

Any input will be greatly appreciated.

Thanks,
Rui

On Tue, Jun 20, 2017 at 8:11 AM, Rui Wang <ruiwang...@gmail.com> wrote:

> Hi Folks,
>
> I got the galaxy docker image and played with it. However, I keep getting
> this when I use dexseq:
>
> Fatal error: Exit code 1 ()
> Could not import pysam, which is needed to process BAM file (though
> not to process text SAM files). Please install the 'pysam' library from
> https://code.google.com/p/pysam/
>
> Looks like there is a conda env that is built on the fly and it doesn't
> have some dependencies installed. If I do the following
>
> biocLite("DEXSeq")
>
> inside the conda-env, then pysam is imported properly. Seems it installs
> the dexseq 1.22. I looked at the package in /tool_deps/_conda/__
> bioconductor-dexseq@1.20.1,
> it's 1.20.1 as the name says. I'm not sure how this could be fixed...my
> thought would be update the conda env dependency to include dexseq 1.22 not
> 1.20, but I'm not familiar with conda...Could someone give me a hand? :-)
>
> Thanks,
> Rui
>
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