Question: Bioconda for R-tool dependencies
0
gravatar for testtoolshed
14 months ago by
testtoolshed30
testtoolshed30 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 • 560 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by testtoolshed30
3
gravatar for Bjoern Gruening
14 months ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k 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 14 months ago by Bjoern Gruening5.1k

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 12 months ago by testtoolshed30
0
gravatar for testtoolshed
14 months ago by
testtoolshed30
testtoolshed30 wrote:

Thank You Bjoern, I will try that

ADD COMMENTlink written 14 months ago by testtoolshed30
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