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Install wgd cli on linux !
By Jit 1409 days ago
(JitMetaENV) ➜ wgd git:(master) pip install --user
ERROR: You must give at least one requirement to install (see "pip help install")
(JitMetaENV) ➜ wgd git:(master) pip install --user .
Processing /home/urbe/sahil_data/novoKorea/comparativeGenomics/wgd
Requirement already satisfied: numpy>=1.16 in /home/urbe/.local/lib/python3.6/site-packages (from wgd==1.2) (1.19.0)
Requirement already satisfied: scipy>=1.2 in /home/urbe/.local/lib/python3.6/site-packages (from wgd==1.2) (1.5.1)
Requirement already satisfied: matplotlib>=3.0.2 in /home/urbe/.local/lib/python3.6/site-packages (from wgd==1.2) (3.2.2)
Collecting bokeh==1.4.0
Downloading bokeh-1.4.0.tar.gz (32.4 MB)
|████████████████████████████████| 32.4 MB 60 kB/s
Requirement already satisfied: six>=1.5.2 in /home/urbe/.local/lib/python3.6/site-packages (from bokeh==1.4.0->wgd==1.2) (1.15.0)
Requirement already satisfied: python-dateutil>=2.1 in /home/urbe/.local/lib/python3.6/site-packages (from bokeh==1.4.0->wgd==1.2) (2.8.1)
Requirement already satisfied: pillow>=4.0 in /home/urbe/anaconda3/envs/JitMetaENV/lib/python3.6/site-packages (from bokeh==1.4.0->wgd==1.2) (8.1.0)
Requirement already satisfied: tornado>=4.3 in /home/urbe/anaconda3/envs/JitMetaENV/lib/python3.6/site-packages (from bokeh==1.4.0->wgd==1.2) (6.1)
Collecting fastcluster==1.1.25
Downloading fastcluster-1.1.25-cp36-cp36m-manylinux1_x86_64.whl (153 kB)
|████████████████████████████████| 153 kB 44.3 MB/s
Collecting joblib==0.11
Downloading joblib-0.11-py2.py3-none-any.whl (176 kB)
|████████████████████████████████| 176 kB 63.7 MB/s
Collecting pandas==0.24.1
Downloading pandas-0.24.1-cp36-cp36m-manylinux1_x86_64.whl (10.1 MB)
|████████████████████████████████| 10.1 MB 38.9 MB/s
Requirement already satisfied: pytz>=2011k in /home/urbe/.local/lib/python3.6/site-packages (from pandas==0.24.1->wgd==1.2) (2020.1)
Collecting biopython>=1.75
Downloading biopython-1.78-cp36-cp36m-manylinux1_x86_64.whl (2.3 MB)
|████████████████████████████████| 2.3 MB 50.3 MB/s
Collecting click>=7.0
Downloading click-7.1.2-py2.py3-none-any.whl (82 kB)
|████████████████████████████████| 82 kB 164 kB/s
Collecting coloredlogs>=10.0
Downloading coloredlogs-15.0-py2.py3-none-any.whl (45 kB)
|████████████████████████████████| 45 kB 727 kB/s
Collecting ete3>=3.1
Downloading ete3-3.1.2.tar.gz (4.7 MB)
|████████████████████████████████| 4.7 MB 47 kB/s
Collecting humanfriendly>=9.1
Downloading humanfriendly-9.1-py2.py3-none-any.whl (86 kB)
|████████████████████████████████| 86 kB 890 kB/s
Collecting Jinja2>=2.7
Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB)
|████████████████████████████████| 125 kB 57.8 MB/s
Collecting MarkupSafe>=0.23
Downloading MarkupSafe-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (27 kB)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/urbe/.local/lib/python3.6/site-packages (from matplotlib>=3.0.2->wgd==1.2) (1.2.0)
Requirement already satisfied: cycler>=0.10 in /home/urbe/.local/lib/python3.6/site-packages (from matplotlib>=3.0.2->wgd==1.2) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/urbe/.local/lib/python3.6/site-packages (from matplotlib>=3.0.2->wgd==1.2) (2.4.7)
Collecting packaging>=16.8
Downloading packaging-20.8-py2.py3-none-any.whl (39 kB)
Collecting plumbum>=1.6.7
Downloading plumbum-1.6.9-py2.py3-none-any.whl (115 kB)
|████████████████████████████████| 115 kB 71.8 MB/s
Collecting progressbar2>=3.39
Downloading progressbar2-3.53.1-py2.py3-none-any.whl (25 kB)
Collecting python-utils>=2.3.0
Downloading python_utils-2.4.0-py2.py3-none-any.whl (12 kB)
Collecting PyYAML>=3.10
Downloading PyYAML-5.3.1.tar.gz (269 kB)
|████████████████████████████████| 269 kB 67.9 MB/s
Collecting seaborn>=0.9.0
Downloading seaborn-0.11.1-py3-none-any.whl (285 kB)
|████████████████████████████████| 285 kB 40.2 MB/s
Collecting sklearn
Using cached sklearn-0.0.tar.gz (1.1 kB)
Collecting scikit-learn
Downloading scikit_learn-0.24.0-cp36-cp36m-manylinux2010_x86_64.whl (22.2 MB)
|████████████████████████████████| 22.2 MB 83 kB/s
Collecting threadpoolctl>=2.0.0
Downloading threadpoolctl-2.1.0-py3-none-any.whl (12 kB)
Building wheels for collected packages: wgd, bokeh, ete3, PyYAML, sklearn
Building wheel for wgd (setup.py) ... done
Created wheel for wgd: filename=wgd-1.2-py3-none-any.whl size=75291 sha256=ebd89070a2b46f55c1191d4daf130d0b1c5d3591d17d7e52020c8c5eccc14863
Stored in directory: /tmp/pip-ephem-wheel-cache-qyjwpfd6/wheels/86/33/fd/c4ff61fc6fbf977d32a25a1c29fc170d9c2e2f15ec4ab06bb8
Building wheel for bokeh (setup.py) ... done
Created wheel for bokeh: filename=bokeh-1.4.0-py3-none-any.whl size=23689200 sha256=5109a280afc85f01827c33d14f705cff39975bc24cd852a3c9efa0bdfb10e403
Stored in directory: /home/urbe/.cache/pip/wheels/b6/72/72/a6a223f72a9b02a4922a3c2fec55b2f65567254d398f6c5f74
Building wheel for ete3 (setup.py) ... done
Created wheel for ete3: filename=ete3-3.1.2-py3-none-any.whl size=2272998 sha256=f8375eb7814bf43d0a0b5289f7508d2ed4c758ba5ee72927afae2ce846b68a0d
Stored in directory: /home/urbe/.cache/pip/wheels/1f/17/0f/fbcffa83fcfad717d040f4de35752ea86cc9106e38c9341f21
Building wheel for PyYAML (setup.py) ... done
Created wheel for PyYAML: filename=PyYAML-5.3.1-cp36-cp36m-linux_x86_64.whl size=44621 sha256=8e0904dc4b0fd5c91d07835dcdec3b8798f39ae0f984b196004d3b9852d0953a
Stored in directory: /home/urbe/.cache/pip/wheels/e5/9d/ad/2ee53cf262cba1ffd8afe1487eef788ea3f260b7e6232a80fc
Building wheel for sklearn (setup.py) ... done
Created wheel for sklearn: filename=sklearn-0.0-py2.py3-none-any.whl size=1316 sha256=a5e80e28bbeac53b7a74d810d197415125d63fcf98ccb88172e55e2234396651
Stored in directory: /home/urbe/.cache/pip/wheels/23/9d/42/5ec745cbbb17517000a53cecc49d6a865450d1f5cb16dc8a9c
Successfully built wgd bokeh ete3 PyYAML sklearn
Installing collected packages: threadpoolctl, MarkupSafe, joblib, scikit-learn, PyYAML, python-utils, pandas, packaging, Jinja2, humanfriendly, sklearn, seaborn, progressbar2, plumbum, fastcluster, ete3, coloredlogs, click, bokeh, biopython, wgd
Attempting uninstall: joblib
Found existing installation: joblib 0.13.2
Uninstalling joblib-0.13.2:
Successfully uninstalled joblib-0.13.2
Attempting uninstall: pandas
Found existing installation: pandas 1.0.5
Uninstalling pandas-1.0.5:
Successfully uninstalled pandas-1.0.5
WARNING: The script humanfriendly is installed in '/home/urbe/.local/bin' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
WARNING: The script ete3 is installed in '/home/urbe/.local/bin' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
WARNING: The script coloredlogs is installed in '/home/urbe/.local/bin' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
WARNING: The script bokeh is installed in '/home/urbe/.local/bin' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Attempting uninstall: biopython
Found existing installation: biopython 1.73
Uninstalling biopython-1.73:
Successfully uninstalled biopython-1.73
WARNING: The script wgd is installed in '/home/urbe/.local/bin' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 PyYAML-5.3.1 biopython-1.78 bokeh-1.4.0 click-7.1.2 coloredlogs-15.0 ete3-3.1.2 fastcluster-1.1.25 humanfriendly-9.1 joblib-0.11 packaging-20.8 pandas-0.24.1 plumbum-1.6.9 progressbar2-3.53.1 python-utils-2.4.0 scikit-learn-0.24.0 seaborn-0.11.1 sklearn-0.0 threadpoolctl-2.1.0 wgd-1.2
Then
(JitMetaENV) ➜ wgd git:(master) export PATH=$PATH:/home/urbe/.local/bin
(JitMetaENV) ➜ wgd git:(master) wgd
