Can't instal MetaPhlAn-3.0.4 : error: [Errno 2] No such file or directory: 'readme.md'

Hi

Try to install but no success.

Regards

root@ubuntu:/opt/MetaPhlAn-3.0.4# python3 setup.py install
/usr/lib/python3.5/distutils/dist.py:261: UserWarning: Unknown distribution option: ‘long_description_content_type’
warnings.warn(msg)
running install
Checking .pth file support in /usr/local/lib/python3.5/dist-packages/
/usr/bin/python3 -E -c pass
TEST PASSED: /usr/local/lib/python3.5/dist-packages/ appears to support .pth files
running bdist_egg
running egg_info
creating MetaPhlAn.egg-info
writing top-level names to MetaPhlAn.egg-info/top_level.txt
writing requirements to MetaPhlAn.egg-info/requires.txt
writing MetaPhlAn.egg-info/PKG-INFO
writing dependency_links to MetaPhlAn.egg-info/dependency_links.txt
writing entry points to MetaPhlAn.egg-info/entry_points.txt
writing manifest file ‘MetaPhlAn.egg-info/SOURCES.txt’
reading manifest file ‘MetaPhlAn.egg-info/SOURCES.txt’
writing manifest file ‘MetaPhlAn.egg-info/SOURCES.txt’
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/metaphlan
copying metaphlan/metaphlan.py -> build/lib/metaphlan
copying metaphlan/strainphlan.py -> build/lib/metaphlan
copying metaphlan/init.py -> build/lib/metaphlan
creating build/lib/metaphlan/utils
copying metaphlan/utils/init.py -> build/lib/metaphlan/utils
copying metaphlan/utils/strain_transmission.py -> build/lib/metaphlan/utils
copying metaphlan/utils/metaphlan2krona.py -> build/lib/metaphlan/utils
copying metaphlan/utils/util_fun.py -> build/lib/metaphlan/utils
copying metaphlan/utils/parallelisation.py -> build/lib/metaphlan/utils
copying metaphlan/utils/plot_tree_graphlan.py -> build/lib/metaphlan/utils
copying metaphlan/utils/sample2markers.py -> build/lib/metaphlan/utils
copying metaphlan/utils/plot_bug.py -> build/lib/metaphlan/utils
copying metaphlan/utils/read_fastx.py -> build/lib/metaphlan/utils
copying metaphlan/utils/merge_metaphlan_tables.py -> build/lib/metaphlan/utils
copying metaphlan/utils/add_metadata_tree.py -> build/lib/metaphlan/utils
copying metaphlan/utils/extract_markers.py -> build/lib/metaphlan/utils
copying metaphlan/utils/external_exec.py -> build/lib/metaphlan/utils
copying metaphlan/utils/pyphlan.py -> build/lib/metaphlan/utils
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/metaphlan
copying build/lib/metaphlan/metaphlan.py -> build/bdist.linux-x86_64/egg/metaphlan
copying build/lib/metaphlan/strainphlan.py -> build/bdist.linux-x86_64/egg/metaphlan
creating build/bdist.linux-x86_64/egg/metaphlan/utils
copying build/lib/metaphlan/utils/init.py -> build/bdist.linux-x86_64/egg/metaphlan/utils
copying build/lib/metaphlan/utils/strain_transmission.py -> build/bdist.linux-x86_64/egg/metaphlan/utils
copying build/lib/metaphlan/utils/metaphlan2krona.py -> build/bdist.linux-x86_64/egg/metaphlan/utils
copying build/lib/metaphlan/utils/util_fun.py -> build/bdist.linux-x86_64/egg/metaphlan/utils
copying build/lib/metaphlan/utils/parallelisation.py -> build/bdist.linux-x86_64/egg/metaphlan/utils
copying build/lib/metaphlan/utils/plot_tree_graphlan.py -> build/bdist.linux-x86_64/egg/metaphlan/utils
copying build/lib/metaphlan/utils/sample2markers.py -> build/bdist.linux-x86_64/egg/metaphlan/utils
copying build/lib/metaphlan/utils/plot_bug.py -> build/bdist.linux-x86_64/egg/metaphlan/utils
copying build/lib/metaphlan/utils/read_fastx.py -> build/bdist.linux-x86_64/egg/metaphlan/utils
copying build/lib/metaphlan/utils/merge_metaphlan_tables.py -> build/bdist.linux-x86_64/egg/metaphlan/utils
copying build/lib/metaphlan/utils/add_metadata_tree.py -> build/bdist.linux-x86_64/egg/metaphlan/utils
copying build/lib/metaphlan/utils/extract_markers.py -> build/bdist.linux-x86_64/egg/metaphlan/utils
copying build/lib/metaphlan/utils/external_exec.py -> build/bdist.linux-x86_64/egg/metaphlan/utils
copying build/lib/metaphlan/utils/pyphlan.py -> build/bdist.linux-x86_64/egg/metaphlan/utils
copying build/lib/metaphlan/init.py -> build/bdist.linux-x86_64/egg/metaphlan
byte-compiling build/bdist.linux-x86_64/egg/metaphlan/metaphlan.py to metaphlan.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/metaphlan/strainphlan.py to strainphlan.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/metaphlan/utils/init.py to init.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/metaphlan/utils/strain_transmission.py to strain_transmission.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/metaphlan/utils/metaphlan2krona.py to metaphlan2krona.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/metaphlan/utils/util_fun.py to util_fun.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/metaphlan/utils/parallelisation.py to parallelisation.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/metaphlan/utils/plot_tree_graphlan.py to plot_tree_graphlan.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/metaphlan/utils/sample2markers.py to sample2markers.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/metaphlan/utils/plot_bug.py to plot_bug.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/metaphlan/utils/read_fastx.py to read_fastx.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/metaphlan/utils/merge_metaphlan_tables.py to merge_metaphlan_tables.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/metaphlan/utils/add_metadata_tree.py to add_metadata_tree.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/metaphlan/utils/extract_markers.py to extract_markers.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/metaphlan/utils/external_exec.py to external_exec.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/metaphlan/utils/pyphlan.py to pyphlan.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/metaphlan/init.py to init.cpython-35.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying MetaPhlAn.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying MetaPhlAn.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying MetaPhlAn.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying MetaPhlAn.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying MetaPhlAn.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying MetaPhlAn.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents…
metaphlan.pycache.metaphlan.cpython-35: module references file
metaphlan.pycache.strainphlan.cpython-35: module references file
metaphlan.utils.pycache.extract_markers.cpython-35: module references file
creating dist
creating ‘dist/MetaPhlAn-3.0.4-py3.5.egg’ and adding ‘build/bdist.linux-x86_64/egg’ to it
removing ‘build/bdist.linux-x86_64/egg’ (and everything under it)
Processing MetaPhlAn-3.0.4-py3.5.egg
removing ‘/usr/local/lib/python3.5/dist-packages/MetaPhlAn-3.0.4-py3.5.egg’ (and everything under it)
creating /usr/local/lib/python3.5/dist-packages/MetaPhlAn-3.0.4-py3.5.egg
Extracting MetaPhlAn-3.0.4-py3.5.egg to /usr/local/lib/python3.5/dist-packages
MetaPhlAn 3.0.4 is already the active version in easy-install.pth
Installing strain_transmission.py script to /usr/local/bin
Installing strainphlan script to /usr/local/bin
Installing read_fastx.py script to /usr/local/bin
Installing sample2markers.py script to /usr/local/bin
Installing add_metadata_tree.py script to /usr/local/bin
Installing extract_markers.py script to /usr/local/bin
Installing merge_metaphlan_tables.py script to /usr/local/bin
Installing plot_tree_graphlan.py script to /usr/local/bin
Installing metaphlan script to /usr/local/bin

Installed /usr/local/lib/python3.5/dist-packages/MetaPhlAn-3.0.4-py3.5.egg
Processing dependencies for MetaPhlAn==3.0.4
Searching for phylophlan
Reading https://pypi.python.org/simple/phylophlan/
Best match: PhyloPhlAn 3.0.1
Downloading https://files.pythonhosted.org/packages/7e/b2/edb462e68b9d9ecc1d9771ad523d14b16811ce706abd4fe7ae489a9b39b4/PhyloPhlAn-3.0.1.tar.gz#sha256=a7ae1e336ff795eb9921b70602528fba1708b9ed9f10ef749b9cc2aae2487b2d
Processing PhyloPhlAn-3.0.1.tar.gz
Writing /tmp/easy_install-8oq_rw32/PhyloPhlAn-3.0.1/setup.cfg
Running PhyloPhlAn-3.0.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-8oq_rw32/PhyloPhlAn-3.0.1/egg-dist-tmp-fu2n58iw
error: [Errno 2] No such file or directory: ‘readme.md’

Blockquote

Have you tried to install it using pip? There are some directives in the setup.py that are not compatible with setuputils.