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(https://stackoverflow.co/labs/) Learn more about Labs (https://cdn.sstatic.net/Sites/stackoverflow/Img/apple-touch-icon.png?v=c78bd457575a) (/questions/50333650/install-python-package-in-docker-file) Install python package in docker file (/questions/ask) Ask Question (2018-05-14 15:09:14Z) Asked 6 years, 3 months ago Modified (?lastactivity) (2023-08-01 02:46:47Z) 1 year, 1 month ago (Viewed 259,090 times) Viewed 259k times This question shows research effort; it is useful and clear (70:3:31e,16:14541f0f57baab6f,10:1725239305,16:7ddb9ffaae30b106,8:50333650,c10542146f2165dac53dd03a459533a77fc49a87b61d61a0edb60a986db15700) 63 (This question does not show any research effort; it is unclear or not useful) (70:3:31e,16:dde6a1ff87cf581e,10:1725239305,16:3049680d8ff0d1c4,8:50333650,ad1bd7b6959983928071f58414757fc61df7309b137b1a7b20614eb90ad82b0e) Save this question. (/posts/50333650/timeline) Show activity on this post. In my docker file, I want to install med2image python package ((https://github.com/FNNDSC/med2image) https://github.com/FNNDSC/med2image ). I use the following code: FROM ubuntu:16.04 RUN apt-get update && apt-get install -y --no-install-recommends \ python3.5 \ python3-pip \ && \ apt-get clean && \ rm -rf /var/lib/apt/lists/* RUN pip install nibabel pydicom matplotlib pillow RUN pip install med2image But I get the following error when I want to build the image: Downloading https://files.pythonhosted.org/packages/6f/e5/948b023c7feb72adf7dfb26d90a13c838737bbf52be704f5ddd0878e3264/med2image-1.1 .2 .tar.gz Complete output from command python setup.py egg_info: Sorry, only Python 3.5 + is supported. ---------------------------------------- Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-install-FnNb_S/med2image/ The command '/bin/sh -c pip install med2image' returned a non-zero code: 1 What should I do?! (/questions/tagged/python) (show questions tagged 'python') python (/questions/tagged/docker) (show questions tagged 'docker') docker (/questions/tagged/dockerfile) (show questions tagged 'dockerfile') dockerfile (/q/50333650) (Short permalink to this question) Share Share a link to this question Copy link (https://creativecommons.org/licenses/by-sa/4.0/) (The current license for this post: CC BY-SA 4.0) CC BY-SA 4.0 (/posts/50333650/edit) () Improve this question Follow (70:3:31e,16:4e74c5124423f3eb,10:1725239305,16:f8d95d14e749fdf7,8:50333650,3a98474da99aa924c80c6197090faaca5e4246fac9801e652708665729ac7b22) Follow this question to receive notifications (/posts/50333650/revisions) (show all edits to this post) edited (2023-08-01 02:46:47Z) Aug 1, 2023 at 2:46 (/users/4197269/user) (user's user avatar) (/users/4197269/user) user (reputation score) 1,242 (1 gold badge) 1 1 gold badge (13 silver badges) 13 13 silver badges (31 bronze badges) 31 31 bronze badges asked (2018-05-14 15:09:14Z) May 14, 2018 at 15:09 (/users/8155727/mehdi) (Mehdi's user avatar) (/users/8155727/mehdi) Mehdi Mehdi (reputation score) 1,266 (1 gold badge) 1 1 gold badge (18 silver badges) 18 18 silver badges (28 bronze badges) 28 28 bronze badges 2 (number of 'useful comment' votes received) 1 Try adding the following to set python3 as default (https://askubuntu.com/questions/320996/how-to-make-python-program-command-execute-python-3) (how to make python program command execute python 3) askubuntu.com/questions/320996/… (in particular the update-alternatives way) – (/users/3165602/oleg-sklyar) (10,002 reputation) Oleg Sklyar Commented (2018-05-14 15:33:01Z, License: CC BY-SA 4.0) May 14, 2018 at 15:33 (this comment was edited 1 time) (number of 'useful comment' votes received) 2 I would suggest to use (https://store.docker.com/images/python) that base image instead (FROM python:3 aka FROM python:3.6.5 ) – (/users/9164010/erikmd) (14,505 reputation) ErikMD Commented (2018-05-14 21:06:42Z, License: CC BY-SA 4.0) May 14, 2018 at 21:06 (Use comments to ask for more information or suggest improvements. Avoid answering questions in comments.) Add a comment | (Expand to show all comments on this post) 4 Answers 4 Sorted by: (/questions/50333650/install-python-package-in-docker-file?answertab=scoredesc#tab-top) Reset to default (scoredesc) Highest score (default) (trending) Trending (recent votes count more) (modifieddesc) Date modified (newest first) (createdasc) Date created (oldest first) This answer is useful (70:3:31e,16:796a7f691ca21e29,10:1725239305,16:adf456b3f8a2a770,8:50339110,3871d02df643635eef8c592677fd24ccc213eaac01a7f56600bf9a59dfdb5368) 89 (This answer is not useful) (70:3:31e,16:95e335e392514c4b,10:1725239305,16:a34440f2914f339c,8:50339110,4d8e4b5eaa5ecfb9c58ff750da5c97a57f7930aa8e51fd1fc096fad68e256207) Save this answer. (Loading when this answer was accepted…) (/posts/50339110/timeline) Show activity on this post. Recommended base image As suggested in my comment, you could write a Dockerfile that looks like: FROM python:3 RUN pip install --no-cache-dir --upgrade pip && \ pip install --no-cache-dir nibabel pydicom matplotlib pillow med2image # Note: we had to merge the two "pip install" package lists here, otherwise # the last "pip install" command in the OP may break dependency resolution… CMD ["cat" , "/etc/os-release" ] And the command example above could confirm at runtime (docker build --pull -t test . && docker run --rm -it test ) that this image is based on the GNU/Linux distribution "Debian stable". Generic Dockerfile template Finally to give a comprehensive answer, note that a good practice regarding Python dependencies consists in specifying them in a declarative way in a dedicated text file (in alphabetical order, to ease review and update) so that for your example, you may want to write the following file: requirements.txt matplotlib med2image nibabel pillow pydicom and use the following generic Dockerfile FROM python:3 WORKDIR /usr/src/app COPY requirements.txt ./ RUN pip install --no-cache-dir --upgrade pip \ && pip install --no-cache-dir -r requirements.txt COPY . . CMD ["python" , "./your-daemon-or-script.py" ] To be more precise, this is the approach suggested in the documentation of the Docker official image (https://hub.docker.com/_/python/) python , §. (https://github.com/docker-library/docs/tree/master/python#how-to-use-this-image) How to use this image (/a/50339110) (Short permalink to this answer) Share Share a link to this answer Copy link (https://creativecommons.org/licenses/by-sa/4.0/) (The current license for this post: CC BY-SA 4.0) CC BY-SA 4.0 (/posts/50339110/edit) () Improve this answer Follow (70:3:31e,16:1a10116fc7696031,10:1725239305,16:8350e512664ea5c9,8:50339110,2d829a71c9412e7803de24a004aafbea176f66d493cdef9a4b8405d13c627430) Follow this answer to receive notifications (/posts/50339110/revisions) (show all edits to this post) edited (2022-09-07 14:25:11Z) Sep 7, 2022 at 14:25 answered (2018-05-14 21:14:59Z) May 14, 2018 at 21:14 (/users/9164010/erikmd) (ErikMD's user avatar) (/users/9164010/erikmd) ErikMD ErikMD (reputation score 14,505) 14.5k (3 gold badges) 3 3 gold badges (38 silver badges) 38 38 silver badges (73 bronze badges) 73 73 bronze badges 7 When RUN python -m pip install --upgrade pip is used, then does it re-use the same layer or does it create new layer (so effectively use upgrade)? – (/users/1779091/variable) (9,313 reputation) variable Commented (2020-05-14 11:15:48Z, License: CC BY-SA 4.0) May 14, 2020 at 11:15 (this comment was edited 1 time) (number of 'useful comment' votes received) 1 (maybe python -m pip install --upgrade pip is unneeded, but) I confirm that the 2 commands concatenated with a && (RUN pip install --upgrade pip && pip install --no-cache-dir -r requirements.txt ) do create a single layer. See also the SO question (https://stackoverflow.com/q/59535609/9164010) Purpose of specifying several UNIX commands in a single RUN instruction in Dockerfile – (/users/9164010/erikmd) (14,505 reputation) ErikMD Commented (2020-05-14 11:33:19Z, License: CC BY-SA 4.0) May 14, 2020 at 11:33 prefere a single pip install command or you might break dependency resolution – (/users/1912465/gaetan) (488 reputation) Gaetan Commented (2022-09-06 09:17:06Z, License: CC BY-SA 4.0) Sep 6, 2022 at 9:17 @Gaetan I guess you talk about theRUN command, but can you be more specific? which exact command would you recommend? – (/users/9164010/erikmd) (14,505 reputation) ErikMD Commented (2022-09-06 11:27:23Z, License: CC BY-SA 4.0) Sep 6, 2022 at 11:27 BTW AFAICT, pip and dependency resolution is not very robust: (independently of this Docker context) I often stumbled on a pip install command that went through successfully, unlike a subsequent pip check … – (/users/9164010/erikmd) (14,505 reputation) ErikMD Commented (2022-09-06 11:28:58Z, License: CC BY-SA 4.0) Sep 6, 2022 at 11:28 (this comment was edited 2 times) (Use comments to ask for more information or suggest improvements. Avoid comments like “+1” or “thanks”.) | (Expand to show all comments on this post) Show 2 more comments This answer is useful (70:3:31e,16:1939a187a5706993,10:1725239305,16:25f063878a6150e3,8:50339177,8c83f19bc632ff46d1f5c84552f8202810493d64dc1fe4421a06dd84af879a25) 46 (This answer is not useful) (70:3:31e,16:5b1a962c744dce49,10:1725239305,16:61f9df3ee4d877ed,8:50339177,a9d5874ae3c7e12918643e9dd771dec63f37f7e3bc07133242c0378e9c4ca887) Save this answer. (Loading when this answer was accepted…) (/posts/50339177/timeline) Show activity on this post. Some of the other answers/comments are suggesting to change your base image but if you want to keep your ubuntu 16.04 you can also simply specify your version of pip/python to use pip3 or pip3.5 like shown below. FROM ubuntu:16.04 RUN apt-get update && apt-get install -y --no-install-recommends \ python3.5 \ python3-pip \ && \ apt-get clean && \ rm -rf /var/lib/apt/lists/* RUN pip3 install nibabel pydicom matplotlib pillow RUN pip3 install med2image (/a/50339177) (Short permalink to this answer) Share Share a link to this answer Copy link (https://creativecommons.org/licenses/by-sa/4.0/) (The current license for this post: CC BY-SA 4.0) CC BY-SA 4.0 (/posts/50339177/edit) () Improve this answer Follow (70:3:31e,16:1f5f62dd7e20bc5e,10:1725239305,16:22de058bd2910154,8:50339177,c95569f43a290d4fbd504f80178f8dd2852d2e054c0e25ddc95c97f828d7bfb8) Follow this answer to receive notifications (/posts/50339177/revisions) (show all edits to this post) edited (2019-09-10 14:11:42Z) Sep 10, 2019 at 14:11 (/users/3514300/tummala-dhanvi) (Tummala Dhanvi's user avatar) (/users/3514300/tummala-dhanvi) Tummala Dhanvi (reputation score) 3,310 (2 gold badges) 2 2 gold badges (22 silver badges) 22 22 silver badges (38 bronze badges) 38 38 bronze badges answered (2018-05-14 21:20:53Z) May 14, 2018 at 21:20 (/users/5050917/mgc) (mgc's user avatar) (/users/5050917/mgc) mgc mgc (reputation score) 5,393 (1 gold badge) 1 1 gold badge (27 silver badges) 27 27 silver badges (38 bronze badges) 38 38 bronze badges 1 (number of 'useful comment' votes received) 1 Is it possible to make the image smaller? – (/users/5978442/jinyu-wu) (95 reputation) Jinyu Wu Commented (2020-01-23 22:56:45Z, License: CC BY-SA 4.0) Jan 23, 2020 at 22:56 (Use comments to ask for more information or suggest improvements. Avoid comments like “+1” or “thanks”.) Add a comment | (Expand to show all comments on this post) This answer is useful (70:3:31e,16:520dad6a592d017d,10:1725239305,16:a55a8cee2dbf30ef,8:50339163,ef72037fed40de5d904a614438797ea9163532906647183de45bb2e128b64f44) 5 (This answer is not useful) (70:3:31e,16:fc76c0c362e30459,10:1725239305,16:7ff17ab578e8c748,8:50339163,373406e27c5cc57274a8a4f739e81fcceb85ff5c6fc983c76786f75f5e853b70) Save this answer. (Loading when this answer was accepted…) (/posts/50339163/timeline) Show activity on this post. Try pip3 RUN pip3 install nibabel pydicom matplotlib pillow RUN pip3 install med2image (/a/50339163) (Short permalink to this answer) Share Share a link to this answer Copy link (https://creativecommons.org/licenses/by-sa/4.0/) (The current license for this post: CC BY-SA 4.0) CC BY-SA 4.0 (/posts/50339163/edit) () Improve this answer Follow (70:3:31e,16:26070dd082f51159,10:1725239305,16:be6a6aa14acf5b8e,8:50339163,c3acece7063e9984f2ebe68c7c24d3185101a9ad26b770b2473dfd465c4d80eb) Follow this answer to receive notifications (/posts/50339163/revisions) (show all edits to this post) edited (2018-05-15 17:06:25Z) May 15, 2018 at 17:06 answered (2018-05-14 21:19:37Z) May 14, 2018 at 21:19 (/users/2170283/d-g) (d g's user avatar) (/users/2170283/d-g) d g d g (reputation score) 1,604 (14 silver badges) 14 14 silver badges (13 bronze badges) 13 13 bronze badges (Use comments to ask for more information or suggest improvements. Avoid comments like “+1” or “thanks”.) Add a comment | (Expand to show all comments on this post) This answer is useful (70:3:31e,16:f1cea6e760a3b2fa,10:1725239305,16:4090fd348ea59e04,8:66107064,f4d4307395d0b568f595401df70e4dabd14019369e3819491ff24530d331c1fa) 2 (This answer is not useful) (70:3:31e,16:013eaed7c6f3a1e9,10:1725239305,16:7bbc42fc4c3b3e69,8:66107064,754730b9698477a770f04c251d2c8dfbc228177c11050e62efc003d24ab610b9) Save this answer. (Loading when this answer was accepted…) (/posts/66107064/timeline) Show activity on this post. If you have Jupyter Notebook in your docker container, you can install any python package by running a new Terminal in Jupyter by clicking the button shown here: (https://i.sstatic.net/3xY9S.png) (button for terminal) and running: pip install The package stays in the docker container even after you exit the container. (/a/66107064) (Short permalink to this answer) Share Share a link to this answer Copy link (https://creativecommons.org/licenses/by-sa/4.0/) (The current license for this post: CC BY-SA 4.0) CC BY-SA 4.0 (/posts/66107064/edit) () Improve this answer Follow (70:3:31e,16:a3d5852dc38895d2,10:1725239305,16:fa2472060ce537ea,8:66107064,c314d3ca1dd9acbe4ab15f320da7de10f704a3ac1f49d4e10197efc0f1388cb2) Follow this answer to receive notifications (/posts/66107064/revisions) (show all edits to this post) edited (2021-02-14 10:44:07Z) Feb 14, 2021 at 10:44 answered (2021-02-08 18:12:05Z) Feb 8, 2021 at 18:12 (/users/9212050/sayyor-y) (Sayyor Y's user avatar) (/users/9212050/sayyor-y) Sayyor Y Sayyor Y (reputation score) 1,240 (3 gold badges) 3 3 gold badges (15 silver badges) 15 15 silver badges (30 bronze badges) 30 30 bronze badges (Use comments to ask for more information or suggest improvements. Avoid comments like “+1” or “thanks”.) 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