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galaxyproject / pulsar

Distributed job execution application built for Galaxy
https://pulsar.readthedocs.io
Apache License 2.0
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Allow overriding amqp prefix that doesn't match the manager name. #315

Closed jmchilton closed 1 year ago

jmchilton commented 1 year ago 
 => ERROR [8/8] RUN _pulsar-conda-init --conda_prefix=/pulsar_dependencie  0.7s 
------                                                                          
 > [8/8] RUN _pulsar-conda-init --conda_prefix=/pulsar_dependencies/conda:      
#12 0.602 Traceback (most recent call last):                                    
#12 0.602   File "/usr/local/bin/_pulsar-conda-init", line 5, in <module>       
#12 0.602     from pulsar.scripts._conda_init import main                       
#12 0.602   File "/usr/local/lib/python3.7/site-packages/pulsar/scripts/_conda_init.py", line 10, in <module>
#12 0.602     from galaxy.tool_util.deps.conda_util import (
#12 0.602   File "/usr/local/lib/python3.7/site-packages/galaxy/tool_util/deps/__init__.py", line 24, in <module>
#12 0.602     from .dependencies import ToolInfo
#12 0.602   File "/usr/local/lib/python3.7/site-packages/galaxy/tool_util/deps/dependencies.py", line 15, in <module>
#12 0.603     from .mulled.mulled_build import DEFAULT_CHANNELS
#12 0.603   File "/usr/local/lib/python3.7/site-packages/galaxy/tool_util/deps/mulled/mulled_build.py", line 25, in <module>
#12 0.603     from galaxy.tool_util.deps.conda_util import (
#12 0.603   File "/usr/local/lib/python3.7/site-packages/galaxy/tool_util/deps/conda_util.py", line 17, in <module>
#12 0.603     from galaxy.util import (
#12 0.603 ImportError: cannot import name 'shlex_join' from 'galaxy.util' (/usr/local/lib/python3.7/site-packages/galaxy/util/__init__.py)
jmchilton commented 1 year ago

The dependencies on ancient pre-release packages was causing less ancient pre-release packages to be brought in and we didn't want that it looks like.

jmchilton commented 1 year ago

I should have been more explicit about this - a huge thanks to @nsoranzo for a lot of this which I ripped out of https://github.com/galaxyproject/pulsar/pull/312 without doing much to preserve credit.