Hi @ebolyen,
Many thanks for your suggestions. I’m not sure I’ve been able to satisfy all of them, though!
It took me a bit, but I now have the conda package of MetaPhlAn2.
You can find it here: https://anaconda.org/fasnicar
And, the commands I used in QIIME2 VM for installing it are:
$ conda install bowtie2 -c bioconda
$ conda install -c fasnicar metaphlan2
I’m not sure why I have to manually install bowtie2, as I thought that the MetaPhlAn2 package would have this information stored within it, but apparently not, or maybe there is another way to specify this while building the package.
I tried to install the MetaPhlAn2 package on my QIIME2 virtual machine but without success. I’m seeing this error:
(qiime2-2017.9) qiime2@qiime2core2017-9:~$ qiime dev refresh-cache
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2017.9/bin/qiime", line 6, in <module>
sys.exit(q2cli.__main__.qiime())
File "/home/qiime2/miniconda/envs/qiime2-2017.9/lib/python3.5/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/home/qiime2/miniconda/envs/qiime2-2017.9/lib/python3.5/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/qiime2/miniconda/envs/qiime2-2017.9/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/qiime2/miniconda/envs/qiime2-2017.9/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/qiime2/miniconda/envs/qiime2-2017.9/lib/python3.5/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/qiime2/miniconda/envs/qiime2-2017.9/lib/python3.5/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/qiime2/miniconda/envs/qiime2-2017.9/lib/python3.5/site-packages/q2cli/dev.py", line 27, in refresh_cache
import q2cli.cache
File "/home/qiime2/miniconda/envs/qiime2-2017.9/lib/python3.5/site-packages/q2cli/cache.py", line 302, in <module>
CACHE = DeploymentCache()
File "/home/qiime2/miniconda/envs/qiime2-2017.9/lib/python3.5/site-packages/q2cli/cache.py", line 61, in __init__
self._state = self._get_cached_state(refresh=refresh)
File "/home/qiime2/miniconda/envs/qiime2-2017.9/lib/python3.5/site-packages/q2cli/cache.py", line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File "/home/qiime2/miniconda/envs/qiime2-2017.9/lib/python3.5/site-packages/q2cli/cache.py", line 200, in _cache_current_state
state = self._get_current_state()
File "/home/qiime2/miniconda/envs/qiime2-2017.9/lib/python3.5/site-packages/q2cli/cache.py", line 238, in _get_current_state
plugin_manager = qiime2.sdk.PluginManager()
File "/home/qiime2/miniconda/envs/qiime2-2017.9/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 44, in __new__
self._init()
File "/home/qiime2/miniconda/envs/qiime2-2017.9/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 58, in _init
plugin = entry_point.load()
File "/home/qiime2/miniconda/envs/qiime2-2017.9/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2316, in load
return self.resolve()
File "/home/qiime2/miniconda/envs/qiime2-2017.9/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2322, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
ImportError: No module named 'metaphlan2.plugin_setup'; 'metaphlan2' is not a package
This is strange as I with the code in the metaphlan2-install repository (https://bitbucket.org/biobakery/metaphlan2-install) I’m able to register the plugin. Does anyone have an idea about what I’m doing wrong with the conda package?
Many thanks for all your help,
Francesco