Generate metadata in separate conda environment

[mvdbeek]

Galaxy supports generating metadata in a separate command (enable
beta_tool_command_isolation). This command has its own dependency resolution,
that may interfere with thedependency resolution of the actual tool, if the
same environment is being used. With this PR we create a new environment when
resolving metadata dependencies with conda, that will be active only for
metadata generation.

Should solve issue #2247

[mvdbeek]

Fyi, the relevant part of the job_script with this PR would look like this:

mkdir -p working; cd working; /Users/marius/src/galaxy/database/jobs_directory/000/313/tool_script.sh; return_code=$?; cd '/Users/marius/src/galaxy/database/jobs_directory/000/313'; [ "$CONDA_DEFAULT_ENV" = "/Users/marius/src/galaxy/database/jobs_directory/000/313/conda-metadata-env" ] || . /Users/marius/conda/bin/activate '/Users/marius/src/galaxy/database/jobs_directory/000/313/conda-metadata-env' 2>&1 ; python "/Users/marius/src/galaxy/database/jobs_directory/000/313/set_metadata_zYlbEg.py" "/Users/marius/src/galaxy/database/tmp/tmpWpUktm" "/Users/marius/src/galaxy/database/jobs_directory/000/313/working/galaxy.json" "/Users/marius/src/galaxy/database/jobs_directory/000/313/metadata_in_HistoryDatasetAssociation_374_qpxnc0,/Users/marius/src/galaxy/database/jobs_directory/000/313/metadata_kwds_HistoryDatasetAssociation_374_9wJNFk,/Users/marius/src/galaxy/database/jobs_directory/000/313/metadata_out_HistoryDatasetAssociation_374_q43IxKSNIP...; sh -c "exit $return_code"
...

whereas the tool_script.sh looks like this:

#!/bin/bash
[ "$CONDA_DEFAULT_ENV" = "/Users/marius/src/galaxy/database/jobs_directory/000/313/conda-env" ] || . /Users/marius/conda/bin/activate '/Users/marius/src/galaxy/database/jobs_directory/000/313/conda-env' 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/Users/marius/src/galaxy/database/jobs_directory/000/313/conda-env" ] || . /Users/marius/conda/bin/activate '/Users/marius/src/galaxy/database/jobs_directory/000/313/conda-env' 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/Users/marius/src/galaxy/database/jobs_directory/000/313/conda-env" ] || . /Users/marius/conda/bin/activate '/Users/marius/src/galaxy/database/jobs_directory/000/313/conda-env' 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/Users/marius/src/galaxy/database/jobs_directory/000/313/conda-env" ] || . /Users/marius/conda/bin/activate '/Users/marius/src/galaxy/database/jobs_directory/000/313/conda-env' 2>&1 ; ln -f -s "/Users/marius/src/galaxy/database/files/_metadata_files/000/metadata_31.dat" alignment.sorted.bam.bai && ln -f -s "/Users/marius/src/galaxy/database/files/000/dataset_297.dat" alignment.sorted.bam SNIP...

[jmchilton]

Beautiful - I think this is a fantastic approach to fixing this problem. Sorry these things we intertwined from the beginning.