Hi Christopher,
due to the old version of Galaxy you need to manually update Conda (conda update conda) and explicitly set the current channel order in your galaxy.ini file, this should be conda_ensure_channels = iuc,conda-forge,bioconda,defaults
With these set you can remove the exisiting conda environment for deseq2 (conda env remove -n mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101) and then re-install deseq2. Once you update to a newer Galaxy version you can comment the conda_ensure_channels setting again and continue using the default channel order that Galaxy ships.
Hope that helps, Marius
On Tue, 18 Sep 2018 at 12:18, Christopher Previti < christopher.previti@dkfz-heidelberg.de> wrote:
Dear all,
I have been trying to get deseq2 (latest version 17, 2018-09-05 from iuc; we are still running on galaxy version 17.09) to work properly but to no avail. Older versions have other errors, I have focused on the latest version.
I get this cryptic error when I run it:
/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/R: symbol lookup error: /opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/../../lib/../../libreadline.so.6: undefined symbol: PC
/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/R: symbol lookup error: /opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/../../lib/../../libreadline.so.6: undefined symbol: PC
Does anybody know what to do about this?
Thanks and best regards,
Christopher
*Dr. Christopher Previti* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) Bioinformatician
German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany Room: B2.102 (INF580/TP3) Phone: +49 6221 42-4661
christopher.previti@dkfz.de http://www.dkfz.de/ www.dkfz.de
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