Dear devs I'm experiencing problems with the conda dependencies for the DESeq2 tool (https://toolshed.g2.bx.psu.edu/repository?repository_id=1f158f7565dc70f9) installed into our production instance.
When this tool is run the only output is: /PATH/TO/job_working_directory/025/25029/conda-env/lib/R/bin/exec/R: symbol lookup error: /PATH/TO/job_working_directory/025/25029/conda-env/lib/R/bin /exec/../../lib/../../libreadline.so.6: undefined symbol: PC I've tried manually reinstalling the two dependencies (bioconductor-deseq2@1.14.2 and r-getopt@1.20.0) by moving the relevant directories from 'tool_dependencies/_conda/envs' and then doing e.g. conda_/bin/conda create -n __r-getopt@1.20.0 --override-channels -c iuc -c bioconda -c conda-forge -c defaults -c r r-getopt=1.20.0 to see if this fixes the problem. However while it completes okay for the bioconductor-deseq2 package, for r-getopt I get the following failure: PaddingError: Placeholder of length '80' too short in package r::r-base-3.2.2-0. The package must be rebuilt with conda-build > 2.0. I've tried doing 'conda_/bin/conda clean -pt' and retrying but I get the same error. Any help to fix this is greatly appreciated, many thanks Best wishes Peter Ps conda version is 4.2.13 and Galaxy is release_17.05; I'm trying to rebuild the conda environments manually because I couldn't see anything within the Galaxy UI which would let me do it there. -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
