I am trying to use Tippecanoe to output shape files to mbtiles. I running on windows and I know Tippecanoe runs on linux. Can anyone tell me the step by step process to run and use tippecanoe on windows?
I had install docker and pulled "jskeates/tippecanoe" whats next and what commend to use to run the process to convert shapefiles to mbtiles
could I download jskeates/tippecanoe for offline use?
I run docker run -it jskeates/tippecanoe /bin/bash in the windows command prompt and then tippecanoe -o test.mbtiles test.shp but I got "tippecanoe: test.mbtiles: unable to open database file"
Related
I work in neuroscience, and I use a cloud platform called Brainlife to upload and download data (linked here, but I don't think knowledge of Brainlife is relevant to this question). I use Brainlife's command line interface to upload and download data on my university's server. In order to use their CLI, I run Singularity with a Docker image created by Brainlife (found here). I run this using the following code:
singularity shell docker://brainlife/cli -B
I also have the file saved on my server account, and can run it like this:
singularity shell brainlifeimage.sif -B
After running one of those commands, I am able to download and upload data, usually successfully. Currently I'm following Brainlife's tutorial to bulk download data. The tutorial uses the command line tool "jq" (link), which isn't on their docker image. I tried installing it within the Singularity shell like this:
apt-get install jq
And it returned:
Reading package lists... Done
Building dependency tree
Reading state information... Done
W: Not using locking for read only lock file /var/lib/dpkg/lock
E: Unable to locate package jq
Is there an easy way to add this one tool to the image? I've been reading over the Singularity and Docker documentations, but Docker is all new to me and I'm really lost.
If relevant, my university server runs on Ubuntu 16.04.7 LTS, and I am using terminal on a Mac laptop running MacOS 11.3. This is my first stack overflow question - please let me know if i can provide any additional info! Thanks so much.
The short, specific answer: jq is portable, so you can just mount it into the image and use it normally. e.g.,
singularity shell -B /path/to/jq:/usr/bin/jq brainlifeimage.sif
The short, general answer: you can't modify the read only image and need to build a new one.
Long answer with several options and specific examples:
Since singularity images are read only, they cannot have persistent changes made to them. This is great for reproducibility, a bit inconvenient if your tools are likely to change often. You can rebuild the image in several ways, though all will require sudo permissions.
Write a new Singularity definition based on the docker image
Create a new definition file (generally called Singularity or something.def), use the current container as a base and add the desired software in the %post section. Then build the new image with: sudo singularity build brainy_jq.sif Singularity
The definition file docs are quite good and highly recommended.
Bootstrap: docker
From: brainlife/cli:latest
%post
apt-get update && apt-get install -y jq
Create a sandbox of the current singularity image, make your changes, and convert back to a read-only image. See the singularity docs on writable sandbox directories and converting images between formats.
# use --sandbox to create a writable singularity image
sudo singularity build --sandbox writable_brain/ brainlifeimage.sif
# --writable must still be used to make changes, and sudo for correct permissions
sudo singularity exec writable_brain/ bash -c 'apt-get update && apt-get install -y jq'
# convert back to read-only image for normal usage
sudo singularity build brainlifeimage_jq.sif writable_brain/
Modify the source docker image locally and build from that. One of the more... creative options. Almost sudo-free, except singularity pull doesn't accept docker-daemon so a sudo singularity build is necessary.
# add jq to a new docker container. the value for --name doesn't matter, but we use it
# in later steps. The entrypoint needs to be overridden in this case as well.
docker run -it --name brainlife-jq --entrypoint=/bin/bash \
brainlife/cli:1.5.25 -c 'apt-get update && apt-get install -y jq'
# use docker commit to create an image from the container so it can be reused
# note that we're using the name of the image set in the previous step
# the output of docker commit is the hash for the newly created image, so we grab that
IMAGE_ID=$(docker commit brainlife-jq)
# tag the newly created image with a more useful name
docker tag $IMAGE_ID brainlife/cli:1.5.25-jq
# here we use docker-daemon instead of docker to build from a locally cached docker image
# instead of looking at docker hub
sudo singularity build brainlife_jq.sif docker-daemon://brainlife/cli:1.5.25-jq
# now check that it all worked as planned
singularity exec brainlife_jq.sif which jq
# /usr/bin/jq
ref: docker commit, using locally cached docker images
Snippet from my Dockerfile:
FROM node:12.18.0
RUN echo "hello world"
RUN psql --version
When I run docker build . I don't see any output from these two commands even if they are not cached. The documentation says that docker build is verbose by default. Why am I not seeing the output from commands? I used to see them before.
The output while building:
=> [7/18] RUN echo "hello world" 0.9s
The output I am seeing after building finishes:
=> CACHED [6/18] RUN apt-get install postgresql -y 0.0s
=> [7/18] RUN echo "hello world" 6.4s
=> [8/18] RUN psql --version 17.1s
The Dockerfile is created from node:12.18.0 which is based on Debian 9.
Docker version 19.03.13, build 4484c46d9d.
The output you are showing is from buildkit, which is a replacement for the classic build engine that docker ships with. You can adjust output from this with the --progress option:
--progress string Set type of progress output (auto, plain, tty). Use plain to show container output
(default "auto")
Adding --progress=plain will show the output of the run commands that were not loaded from the cache. This can also be done by setting the BUILDKIT_PROGRESS variable:
export BUILDKIT_PROGRESS=plain
If you are debugging a build, and the steps have already been cached, add --no-cache to your build to rerun the steps and redisplay the output:
docker build --progress=plain --no-cache ...
If you don't want to use buildkit, you can revert to the older build engine by exporting DOCKER_BUILDKIT=0 in your shell, e.g.:
DOCKER_BUILDKIT=0 docker build ...
or
export DOCKER_BUILDKIT=0
docker build ...
Just use this flag --progress=plain after build.
For example:
docker-compose build --progress=plain <container_name>
OR
docker build --progress=plain .
If you don't want to use this flag every time, then permanently tell docker to use this flag by doing:
export BUILDKIT_PROGRESS=plain
Here is the official documentation when you type docker build --help.
--progress string Set type of progress output (auto, plain, tty). Use plain to show container output (default "auto")
In Docker 20.10 i had to use the --no-cache flag, too. Otherwise cached output is not shown.
docker build --progress=plain --no-cache .
As an alternative to specifying the --progress=plain option, you can also permanently disable the "pretty" output by setting this env variable in your shell config:
export BUILDKIT_PROGRESS=plain
Do 2 things
Instead of docker build . use this
docker build . --progress=plain
Add random junk to your RUN command every build (this tricks docker into thinking it hasn't seen the command before, so it doesn't use the cached version)
Example. If your command is RUN ls use this instead RUN ls && echo sdfjskdflsjdf (change the sdfjskdflsjdf to something else each time you build).
Why this works
I tried other answers and they all presented problems and imperfections. It's highly frustrating that Docker doesn't have some simple functionality like --verbose=true.
Here's what I ended up using (it's ludicrous but it works).
Suppose you want to see the output of ls command, this won't work docker build .
RUN ls
but this will print the output docker build --progress=plain:
RUN ls
now try again, it won't print! - that's because docker caches the unchanged layer, so the trick is to alter the command each time by adding some nonsense to it && echo sdfljsdfljksdfljk, and changing the nonsense each time docker build --progress=plain:
# This prints
RUN ls && echo sdfljsdfljksdfljk
# Next time you run it use a different token
RUN ls && echo sdlfkjsldfkjlskj
So each and every time, I mash the keyboard and come up with a new token. Stupifying. (note that I tried something like && openssl rand -base64 12 to generate a random string, but docker realises the code hasn't changed that doesn't work).
This solution is highly inferior to genuine docker support for printing output to console.
If your error looks something like this:
#7 0.584 /bin/sh: 1: /install.sh: not found
it's telling you the error is in line number 1. you are running into windows line endings
I was using VS code and I solved it pretty easily by converting the file from CRLF to LF using VS code.
just click on the CRLF button in the bottom right corner of the editor and save the file.
everything should work fine when you build the image now.
I'm trying to do an offline deployment of a docker image with RPM on CentOS.
My spec file is pretty simple :
Source1: myimage.tar.gz
...
%install
cp %{SOURCE1} ...
...
%post
docker load -i myimage.tar.gz
docker-compose up -d
docker image prune -af
I compress my image using docker save and gzip. Then, on another machine, I just load the image with docker and use docker-compose to run my service.
When executing the commands "docker load" and "docker-compose up", I got that error:
sudo: unable to execute /bin/docker: Permission denied
sudo: unable to execute /bin/docker-compose: Permission denied
sudo: unable to execute /bin/docker: Permission denied
My user is part of the docker group, I checked if the RPM file was executed using root, it is...
If I run the RPM on my dev machine, it works, if I execute the commands in a script that is not part of the RPM, it works...
Any ideas ?
Thanks in advance.
You're probably being blocked by SELinux. You can temporarily disable it to check with setenforce 0.
If that is the problem (it is; this is a comment turned into an answer), some possible solutions:
You might be able to use audit2allow to change the denials into new rules to import.
Maybe udica will help. I don't know enough about it to tell.
I tried the first solution and it worked ! grep rpm_script_t /var/log/audit/audit.log | audit2allow -m mypolicy > mypolicy.te
The problem came from the fact that the RPM scripts didn't have the access to the container_runtime_exec_t:file entrypoint that I suppose, allow it to run containers like docker.
Thanks a lot for the tip !
I am trying to set up a Docker image (my Dockerfile is available here, sorry for the french README: https://framagit.org/Gwendal/firefox-icedtea-docker) with an old version of Firefox and an old version of Java to run an old Java applet to start a VPN. My image does work and successfully allows me to start the Java applet in Firefox.
Unfortunately, the said applet then tries to run the following command in the container (I've simply removed the --config part from the command as it does not matter here):
INFO: launching '/usr/bin/pkexec sh -c /usr/sbin/openvpn --config ...'
Then the applet exits silently with an error. While investigating, I've tried running a command with pkexec with the same Docker image, and it gives me this result:
$ sudo docker-compose run firefox pkexec /firefox/firefox-sdk/bin/firefox-bin -new-instance
**
ERROR:pkexec.c:719:main: assertion failed: (polkit_unix_process_get_start_time (POLKIT_UNIX_PROCESS (subject)) > 0)
But I don't know polkit at all and cannot understand this error.
EDIT: A more minimal way to reproduce the problem is with this Dockerfile:
FROM ubuntu:16.04
RUN apt-get update \
&& apt-get install -y policykit-1
And then run:
$ sudo docker build -t pkexec-test .
$ sudo docker run pkexec-test pkexec echo Hello
Which leads here again to:
ERROR:pkexec.c:719:main: assertion failed: (polkit_unix_process_get_start_time (POLKIT_UNIX_PROCESS (subject)) > 0)
Should I conclude that pkexec cannot work in a docker container? Or is there any way to make this command work?
Sidenote: I have no control whatsoever on the Java applet that I try to run, it is a horrible and very dated proprietary black box that I am supposed to use at work, for which I have no access to the source code, and that I must use as is.
I have solved my own problem by replacing pkexec by sudo in the docker image, and by allowing passwordless sudo.
Given an ubuntu docker image where a user called developer was created and configured with a USER statement, add these lines:
# Install sudo and make 'developer' a passwordless sudoer
RUN apt-get install sudo
ADD ./developersudo /etc/sudoers.d/developersudo
# Replacing pkexec by sudo
RUN rm /usr/bin/pkexec
RUN ln -s /usr/bin/sudo /usr/bin/pkexec
with the file developersudo containing:
developer ALL=(ALL) NOPASSWD:ALL
This replaces any call to pkexec made in a process running in the container, by a call to sudo without any password prompt, which works nicely.
I'm running this docker image to use the TICK Kapacitor locally.
The problem I face is that when I try to use User Defined Functions, e.g any of these examples I get the error message that /usr/bin/python2 does not exist.
I add the following to the kapacitor.conf:
[udf.functions]
[udf.functions.tTest]
prog = "/usr/bin/python2"
args = ["-u", "/tmp/kapacitor_udf/mirror.py"]
timeout = "10s"
[udf.functions.tTest.env]
PYTHONPATH = "/tmp/kapacitor_udf/kapacitor/udf/agent/py"
Further attempts from my side including altering the image used to build Kapacitor to install python works but the agent seems to fail to compile anyway.
Is there anyone who managed to get UDFs running using the Kapacitor Docker image?
Thanks
Docker image from the official repository: docker pull kapacitor does not have python installed inside. You can verify this by running shell in the container:
PS> docker exec -it kapacitor bash
and execute one of the command options:
$ python -VERSION
$ python: command not found
or
$ readlink -f $(which python) | xargs -I% sh -c 'echo -n "%:"; % -V'
$ readlink: missing operand
or
$ find / -type f -executable -iname 'python *'
void returns. And oppositely if python is available, commands return version and list of executable files
Note: Here and further all command snippets are given for Powershell on Windows. And all command snippets inside docker container are given for bash shell as Linux images are used.
Basicly, there is two options to get kapacitor image with python inside to execute UDFs:
Install the python in the kapacitor image, i.e. build new docker image from very kapacitor image.
Example could be found here:
Build a new verion of kapacitor image from one of the python official images
The second option is more natural as you get consistent python installation and keep efforts on doing work of installing python which already done by the docker community.
So following option 2 we'll perform:
Examine the Dockefile of the official kapacitor image
Choose an appropriate python image
Create new project and Dockerfile for kapacitor
Build and Check the kapacitor image
Examine Dockefile of official kapacitor image
General note:
For any image, the original Dockerfiles can be obtained in this way:
https://hub.docker.com/
-> Description Tab
-> Supported tags and respective Dockerfile links section
-> each of the tags is a link that leads to the Dockerfile
So for kapacitor everything is in the influxdata-docker git repository
Then in the Dockerfile we find that the image is created based on
FROM buildpack-deps: stretch-curl
here:
buildpack-deps
the image provided by the project of the same name https://hub.docker.com/_/buildpack-deps
curl
This variant includes just the curl, wget, and ca-certificates packages. This is perfect for cases like the Java JRE, where downloading JARs is very common and
necessary, but checking out code isn't.
stretch
short version name of the OS, in this case Debian 9 stretch https://www.debian.org/News/2017/20170617
Buildpack-deps images are in turn built based on
FROM debian: stretch
And Debian images from the minimum docker image
FROM: scratch
Choose appropriate python image
Among python images, for example 3.7, you can find similar versions inheriting from buildpack-deps
FROM buildpack-deps: stretch
Following the inheritance, we'll see:
FROM buildpack-deps: stretch
FROM buildpack-deps: stretch-smc
FROM buildpack-deps: stretch-curl
FROM debian: stretch
In other words, the python: 3.7-stretch image only adds functionality to the Debian compared to the kapacitor image.
This means that we can to rebuild kapacitor image on top of the python image: 3.7-stretch with no risk or gaining incompatibility.
Docker context folder preparation
Clone the repository
https://github.com/influxdata/influxdata-docker.git
Create the folder influxdata-docker/kapacitor/1.5/udf_python/python3.7
Copy the following three files into it from influxdata-docker/kapacitor/1.5/:
Dockerfile
entrypoint.sh
kapacitor.conf
In the copied Dockerfile FROM buildpack-deps: stretch-curl replace with FROM python: 3.7-stretch
Be carefuly! If we work on Windows and because of scientific curiosity open the entrypoint.sh file in the project folder, then be sure to check that it does not change the end-line character from Linux (LF) to Windows variant: (CR LF).
Otherwise, when you start the container later, you get an error:
or in the container log:
exec: bad interpreter: No such file or directory
or if you'll start debugging and, running the container with bash, will do:
$ root # d4022ac550d4: / # exec /entrypoint_.sh
$ bash: /entrypoint_.sh: / bin / bash ^ M: bad interpreter: No such file or directory
Building
Run PS> docker build -f. \ Dockerfile -t kapacitor_python_udf
Again, in case of Windows environment
If during the build execution an error occurs of the form:
E: Release file for http://security.ubuntu.com/ubuntu/dists/bionic-security/InRelease is not valid yet (invalid for another 9h 14min 10s). Updates for this repository will not be applied.
then your computer clock probably went out of sync and/or Docker Desktop incorrectly initialized the time after the system returned from sleep. See the issue)
To fix it, restart Docker Desktop and / or Windows settings -> Date and time settings -> Clock synchronization -> perform Sync
You can also read more here
Launch and check
Launching the container with the same actions as for the standard image. Example:
PS> docker run --name=kapacitor -d `
--net=influxdb-network `
-h kapacitor `
-p 9092:9092 `
-e KAPACITOR_INFLUXDB_0_URLS_0=http://influxdb:8086 `
-v ${PWD}:/var/lib/kapacitor `
-v ${PWD}/kapacitor.conf:/etc/kapacitor/kapacitor.conf:ro `
kapacitor
Check:
PS> docker exec -it kapacitor_2 bash
$ python -VERSION
$ Python 3.7.7
$ readlink -f $(which python) | xargs -I% sh -c 'echo -n "%:"; % -V'
$ /usr/local/bin/python3.7: Python 3.7.7