Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 51050653b44c24328d9225b69d9b1b6971b0354c https://github.com/galaxyproject/galaxy/commit/51050653b44c24328d9225b69d9b1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-06 (Sun, 06 Nov 2016) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Rework dependency shell command handling The approach is to always log a warning with stdout and stderr when the exit code is not 0. With this change, one can expect logs like the follwing: ``` galaxy.tools.deps.conda_util DEBUG 2016-11-05 15:14:17,373 Executing command: /home/mvandenb/miniconda3/bin/conda create -y --name __bowtie@0.12.7 bowtie=0.12.7 127.0.0.1 - - [05/nov./2016:15:14:19 +0200] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://127.0.0.1:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.90 Safari/537.36" 127.0.0.1 - - [05/nov./2016:15:14:22 +0200] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://127.0.0.1:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.90 Safari/537.36" galaxy.tools.deps.conda_util WARNING 2016-11-05 15:14:24,029 Failed to execute command-line /home/mvandenb/miniconda3/bin/conda create -y --name __bowtie@0.12.7 bowtie=0.12.7, stderr was: -------->>begin stderr<<-------- PackageNotFoundError: Package not found: '' Package missing in current linux-64 channels: - bowtie 0.12.7* You can search for packages on anaconda.org with anaconda search -t conda bowtie You may need to install the anaconda-client command line client with conda install anaconda-client -------->>end stderr<<-------- -------->>begin stdout<<-------- Fetching package metadata ............... Solving package specifications: . -------->>end stdout<<-------- galaxy.tools.deps.resolvers.conda DEBUG 2016-11-05 15:14:24,030 Removing failed conda install of bowtie, version '0.12.7' ``` This should be helpful for the more obscure errors that can occur with conda. Commit: bfabe00ea8f07782f0af307b124da8090f2906f2 https://github.com/galaxyproject/galaxy/commit/bfabe00ea8f07782f0af307b124da... Author: John Chilton <jmchilton@gmail.com> Date: 2016-11-13 (Sun, 13 Nov 2016) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3129 from mvdbeek/conda_error_reporting Pass dependency shell command errors to log Compare: https://github.com/galaxyproject/galaxy/compare/7955077e635f...bfabe00ea8f0