https://bioinformaticsonline.com/snippets/view/42617/install-wgd-cli-on-linux? https://bioinformaticsonline.com/snippets/view/42617/install-wgd-cli-on-linux Wed, 13 Jan 2021 18:34:19 -0600 https://bioinformaticsonline.com/snippets/view/42617/install-wgd-cli-on-linux (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]]> Jit