I am working on a station where internet communication is forbidden. Is it possible to install snakemake without conda?
Thanks,
Michelle
Yes, it can be installed via pip as well. However, that still needs a download. With conda, you should also be able to download the package and all dependencies via anaconda.org, and then copy it over to that machine. But it certainly will require some manual steps. There is also a docker container. This is probably easier, because it is only a single file.
Related
I was trying to install Ursina but I was having trouble getting all the required packages I needed to run my code properly. Come to find out, there's a package that refuses to install called 'psd-tools3' that won't install, no matter what I do.
I've been using cmd commands like 'pip install psd-tools3' and 'pip3 install psd-tools3' but no other commands work (i.e. 'sudo pip install psd-tools3' doesn't work because my PC doesn't know what 'sudo' means and doesn't run). I've tried installing required packages for this package, but nothing works. It just keeps giving me this error:
enter image description here
I would really appreciate the help with this problem. All I can really assume is that the Python file '_version' hasn't been created and that's what's throwing the whole program off. If there is a way to add this manually and then install it, I would appreciate steps to do that as well.
I was running this on a Lenovo Thinkpad (Windows 10) on Python 3.10 (I also have Python 3.8.3 but that was installed with the 3.10) and I made sure all packages and pip are up-to-date. Still having this problem and I don't know why.
Seems to me like the issue is on the side of the maintainers of psd-tools3.
For example, looking at the content of the latest source distribution on PyPI, we can see that it does not contain any _version.py file.
This needs to be solved by the project's maintainers, but they do not have a ticket tracker. On the other hand there seems to be an "Author" email address on the project's PyPI page as well as in the project's setup.py script.
A solution might be to clone the project's source code repository (with git), and try to install from the local clone.
Just simply try
pip install psd-tools3==1.9.0
Or
pip install psd-tools3==1.8.2
This should work on your pc as well. I was having same issue, and then I tried this It worked for me
I want to use the package "Dask", but there is one problem.
"Dask dataframe requirements are not installed."
Obviously, we can use pip install "dask[dataframe]" or pip install "dask[complete]".
However, in the secured server where I work, there is no internet connection.
So, I transfer the file of package and install manually.
But, I cannot find the package dask[dataframe] for downloading.
How can I install the rest of packages manually without internet connection?
Thank you
You should look at the setup.py requirements file in the dask repository to see which dependencies it requires.
I'm trying to install TeamViewer by going to their website and downloading the latest version. However, when I open a terminal, navigate to the folder, and enter
sudo dpkg -i teamviewer_13.0.6634_amd64.deb
I get a message that certain dependencies are missing, including qtdeclarative5-qtquick2-plugin. I then installed that, re-ran the install, and there are many other missing dependencies, so I try to just run
sudo apt install qtdeclarative5-*
and this tells me that several dependencies from qml are needed, so I run
sudo apt install qml-module-*
and this again tells me I first need other missing dependencies, and at this point I feel like I am in an endless maze. Is there any efficient way of getting the dependencies that I need? Or am I supposed to be doing something completely different to install TeamViewer? I'm running Linux Mint 18.3 Cinnamon.
Why not use VNC?
This is a question more relevant for ServerFault, Stack Overflow's sister site for IT.
I would like to create a Conda environment from a .yaml file on an offline machine (i.e. no Internet access). On an online machine this works perfectly fine:
conda env create -f environment.yaml
However, it doesn't work on an offline machine as the packages are then not found. How do I do this?
If that's not possible is there another easy way to get my complete Conda environment to an offline machine (including both Conda and pip installed packages)?
Going through the packages one by one to install them from the .tar.bz2 files works, but it is quite cumbersome, so I would like to avoid that.
If you can use pip to install the packages, you should take a look at devpi, particutlarily its server. devpi can cache packages normally installed from PyPI, so only on first install it actually retrieves them. You have to configure pip to retrieve the packages from the devpi server.
As you don't want to list all the packages and their dependencies by hand you should, on a machine connected to the internet:
install the devpi server (I have that running in a Docker container)
run your installation
examine the devpi repository and gathered all the .tar.bz2 and .whl files out of there (you might be able to tar the whole thing)
On the non-connected machine:
Install the devpi server and client
use the devpi client to upload all the packages you gathered (using devpi upload) to the devpi server
make sure you have pip configured to look at the devpi server
run pip, it will find all the packages on the local server.
devpi has a small learning curve, which already worth traversing because of the speed up and the ability to install private packages (i.e. not uploaded to PyPI) as a normal dependency, by just generating the package and upload it to your local devpi server.
I guess that Anthon's solution above is pretty good but just in case anybody is interested in an easy solution that worked for me:
I first created a .yaml file specifying the environment using conda env export > file.yaml. Following the instructions on http://support.esri.com/en/technical-article/000014951, I automatically downloaded all the necessary installation files for conda installed packages and created a channel from the files. For that, I just adapted the code from the link above to work with my .yaml file instead of the conda list file they used. In addition, I automatically downloaded the necessary files for the pip installed packages by looping through the pip entries in the .yaml file and using pip download for downloading each of them. Furthermore, I automatically created separate conda and pip requirement lists from the .yaml file. Then I created the environment using conda create with the offline flag, the file with the conda requirements and my custom channel. Finally, I installed the pip requirements using pip install with the pip requirements file and the folder containing the pip installation files for the option --find-links.
That worked for me. The only problem is that you can only download binaries with pip download if you need to specify a different operating system than the one you are running, and for some packages no binaries are available. That was okay for me now as the target machine has the some characteristics but might be problem in the future, so I am planning to look into the solution suggested by Anthon.
I found the following guide:
http://mark.reid.name/sap/setting-up-clojure.html
but it seems like a whole lot of manual steps, and I bet it is out of date already. Installing ClojureBox on Windows was a breeze. Does anyone know of a simple installer for it? Where can I download it, and what are the steps?
Thanks!
EDIT: Tried installing cake, got:
$ sudo gem install cake
Password:
ERROR: While executing gem ... (Gem::RemoteSourceException)
HTTP Response 302
Also tried installing using the script:
$ sudo ./cake_install.rb
http://github.com/ninjudd/cake-standalone/raw/master/jars/cake-0.5.4.jar
[=============================================================================]
http://build.clojure.org/releases/org/clojure/clojure/1.2.0/clojure-1.2.0.jar
[=============================================================================]
Exception in thread "main" java.lang.UnsupportedClassVersionError: Bad version number in .class file (ordered_set.clj:1)
EDIT 2: Now the Java version issues :) What version of Java do I need and where to download it?
$ sudo cake test
Exception in thread "main" java.lang.UnsupportedClassVersionError: Bad version number in .class file (ordered_set.clj:1)
My Leopard software is up to date :(
Apple Computer supplies their own version of Java. Use the Software Update feature (available on the Apple menu) to check that you have the most up-to-date version of Java for your Mac. If you have problems with downloading, installing or using Java on Mac, please contact Apple Computer Technical Support.
EDIT: Hm ... I suspect that one of the suggestions I tried broke my ability to connect to the internet (both wired as well as wireless) on Apple :(
Clojure is also installable via Homebrew:
http://github.com/mxcl/homebrew
brew install clojure
If you just want to run clojure programs, then macports works. Bear in mind you're dependent upon the maintainer to update versions.
If you plan on writing clojure programs, then cake is a better starting point. Installation involves one of the following (your choice):
Using gem (easiest)
gem install cake
Standalone script
Download the script
Put it somewhere in your path and chmod +x cake to make it executable
Git repository
git clone git://github.com/ninjudd/cake.git
Symlink bin/cake into your path and make it executable
Cake is a full build system, but you can just use it to fire up the repl by running cake repl. There's also leiningen, but starting repls will feel faster in cake since it uses persistent JVMs.
I find Leiningen very easy to use. Just download the script, put it somewhere in your $PATH (/usr/bin/ for example) and make it executable: sudo chmod +x lein.
Now type lein repl and Leiningen will download all the files you need and create a REPL for you. It's that easy.
You may want to check CounterClockWise (an Eclipse plugin). There's a video on how to install it here. It'll give you a lot of features to play with - including a clojure REPL.
Just checked this will still work under Ubuntu. It should be the same for macs, except using whatever macs use instead of apt-get to install maven:
http://www.learningclojure.com/2010/08/clojure-emacs-swank-slime-maven-maven.html
You need to install maven, create a file, then you can just call mvn clojure:repl and everything should just work.
If you'd also like the whole emacs-swank-slime setup that's also easy now, and described there.
If you try it can you comment back here or on the blog to let me know if there are any changes I need to make for macs?
Install MacPorts and then run sudo port install clojure
I once created a package called ClojureX that was partly based on Mark's article. It's not actively maintained anymore (at least not by me), but there's no reason it wouldn't work:
http://github.com/citizen428/ClojureX