Dependencies issue with tool installation via ephemeris
Hello, I got a new Galaxy install using 17.01 latest. I wanted to get the same tools as are in Galaxy main. I installed ephemeris with pip, used get-tool-list to get a yml file with tools, and then shed-install to my Galaxy server. After a few hours, 452 tools got successfully installed, 0 skipped and 0 errored. However, when looking at Galaxy's "manage installed tools", all of the tools that have dependencies are in gray state - missing dependencies. (and error out if ran). If I select a tool, and go to "repository actions", "manage tool dependencies", I see that dependencies are marked as never installed. If I select dependencies and click install, they install - really fast (too fast?), and then that tool works fine... but I'm trying to avoid manually telling each tool to install dependencies - there are a lot of them :) Any suggestions?
Hi, please make sure you have set "install_resolver_dependencies: True" https://github.com/bgruening/docker-galaxy-ngs-preprocessing/blob/master/ngs... This will install you all conda dependencies. Btw. you can also use Galaxy 17.05. 17.09 will be released soon and also can need some testing :) Cheers, Bjoern On 06.09.2017 03:54, RMSe17 wrote:
Hello, I got a new Galaxy install using 17.01 latest. I wanted to get the same tools as are in Galaxy main. I installed ephemeris with pip, used get-tool-list to get a yml file with tools, and then shed-install to my Galaxy server. After a few hours, 452 tools got successfully installed, 0 skipped and 0 errored. However, when looking at Galaxy's "manage installed tools", all of the tools that have dependencies are in gray state - missing dependencies. (and error out if ran). If I select a tool, and go to "repository actions", "manage tool dependencies", I see that dependencies are marked as never installed. If I select dependencies and click install, they install - really fast (too fast?), and then that tool works fine... but I'm trying to avoid manually telling each tool to install dependencies - there are a lot of them :)
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Hello everyone, I have a question about https://github.com/nturaga/bioc-galaxy-integration I am trying to convert a RScript into a Galaxy tool. planemo bioc_tool_init --rscript ./countsAroundTSS.R --input ENCFF027UTM.bam --input mm10 --input 500 --input 500 --input transcripts_mm10_UCSC.sqlite --output ENCFF027UTM.txt --test_case Can only use the --test_case option if also specifying --example_command planemo bioc_tool_init --rscript ./countsAroundTSS.R --example_command "Rscript countsAroundTSS.R--input ENCFF027UTM.bam --input mm10 --input 500 --input 500 --input transcripts_mm10_UCSC.sqlite --output ENCFF027UTM.txt” Error: no such option: --example_command I am able to build a tool is I just run planemo bioc_tool_init --rscript ./countsAroundTSS.R --input ENCFF027UTM.bam --input mm10 --input 500 --input 500 --input transcripts_mm10_UCSC.sqlite --output ENCFF027UTM.txt https://github.com/galaxyproject/planemo/issues/718 Thank you, Deepak
Thanks for your help Bjorn, I was already setting install_resolver_dependencies to True, but I looked at the example you referenced, and saw couple other options that I didn't have set (I didn't see them mentioned in the ephemeris documentation). Once I set the following in the tools yml list, everything started working correctly. install_tool_dependencies: True install_repositoty_dependencies: True Interestingly according to the comments in the example, these should be defaulting to true anyway, but I had to set them explicitly. Thanks again for your help!
Hi, On 13.09.2017 21:15, RMSe17 wrote:
Thanks for your help Bjorn, I was already setting install_resolver_dependencies to True, but I looked at the example you referenced, and saw couple other options that I didn't have set (I didn't see them mentioned in the ephemeris documentation).
Once I set the following in the tools yml list, everything started working correctly. install_tool_dependencies: True
This should not be needed, it will install old tool dependencies, which are deprecated. Which Galaxy version are you using, depending on this the defaults might change. Cheers, Bjoern
install_repositoty_dependencies: True
Interestingly according to the comments in the example, these should be defaulting to true anyway, but I had to set them explicitly.
Thanks again for your help!
Bjoern, Looks like some tools install fine without the "install_tool_dependencies: True" but others come up with dependencies missing. I wonder if some tools are older and are missing something in conda? That's just a guess on my part. Using 17.01 latest, so yea defaults could be different. Thanks!
On 14.09.2017 00:10, RMSe17 wrote:
Bjoern,
Looks like some tools install fine without the "install_tool_dependencies: True" but others come up with dependencies missing. I wonder if some tools are older and are missing something in conda? That's just a guess on my part.
This can very well be! Which tool is this? Cheers, Bjoern
Using 17.01 latest, so yea defaults could be different.
17.05 is recent and 17.09 will be released soon! Cheers, Bjoern
Thanks!
participants (3)
-
Björn Grüning -
Deepak Tanwar -
RMSe17