Question: Bioconda for R-tool dependencies
0
gravatar for testtoolshed
8 months ago by
testtoolshed20
testtoolshed20 wrote:

Hello, I have been trying bioconda for R-tool dependencies for few of packages It is work perfectly but one of my tool need rentrez package (I've tried entrez-direct but I think It is something bit different). What should I do in that case? I've normally use this website for dependency https://bioconda.github.io/recipes

dependencies bioconda R • 342 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by testtoolshed20
3
gravatar for Bjoern Gruening
8 months ago by
Bjoern Gruening4.8k
Germany
Bjoern Gruening4.8k wrote:

Hi,

you could try to contribute your own conda package. We have written some documentation here: https://bioconda.github.io/contributing.html

For normal cran R packages have a look at https://bioconda.github.io/guidelines.html#r-cran. Hope that gets you started!

Cheers, Bjoern

ADD COMMENTlink written 8 months ago by Bjoern Gruening4.8k

Hi, I contribute r-rentrez on bioconda and received fatal error on galaxy: Exit code 127 () /srv/galaxy/server/database/jobs/006/6814/conda-env/lib/R/bin/exec/R: symbol lookup error: /srv/galaxy/server/database/jobs/006/6814/conda-env/lib/R/bin/exec/../../lib/../../libreadline.so.6: undefined symbol: PC

In addition I want to use existing bioconductor-minfi package with mine bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 . Galaxy install only minfi package and return error again 'cannot load annotation package IlluminaHumanMethylation450kanno.ilmn12.hg19'.

Can someone help me with this? (I've tried to install both on my computer and everything works fine)

ADD REPLYlink written 6 months ago by testtoolshed20
0
gravatar for testtoolshed
8 months ago by
testtoolshed20
testtoolshed20 wrote:

Thank You Bjoern, I will try that

ADD COMMENTlink written 8 months ago by testtoolshed20
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