I need to install version 4.7.0 of snakemake, but I cannot find it. Could you please tell me where can I get old versions of the software? I tried the bitbucket repository but I could not find any other than the latest version.
It is available through conda:
$ conda search -c bioconda -f snakemake=4.7.0
Loading channels: \ conda search -c bioconda -f snakemake=4.7
# Name Version Build Channel
snakemake 4.7.0 py35_0 bioconda
snakemake 4.7.0 py36_0 bioconda
Did you try pip?
pip install snakemake==4.7.0
For source code download: https://bitbucket.org/snakemake/snakemake/downloads/?tab=tags
Related
I have been trying to install TensorFlow on my Macbook Air with a M1 chip.
Using Python 3.9.7.
Originally was on MacOS 11, but subsequently upgraded to 12.01
At first, I tried these instructions [https://towardsdatascience.com/installing-tensorflow-on-the-m1-mac-410bb36b776] but got stuck when trying to execute
pip3 install --upgrade --force --no-dependencies https://github.com/apple/tensorflow_macos/releases/download/v0.1alpha3/tensorflow_addons_macos-0.1a3-cp38-cp38-macosx_11_0_arm64.whl https://github.com/apple/tensorflow_macos/releases/download/v0.1alpha3/tensorflow_macos-0.1a3-cp38-cp38-macosx_11_0_arm64.whl
ERROR: tensorflow_addons_macos-0.1a3-cp38-cp38-macosx_11_0_arm64.whl is not a supported wheel on this platform.
So I tried to follow these instructions [https://www.tensorflow.org/install/source#macos_1] to compile TensorFlow, but when I try
bazel build //tensorflow/tools/pip_package:build_pip_package
I get these errors:
ERROR: /Users/scottbrown/tensorflow/tensorflow/lite/python/BUILD:62:10: Target '//tensorflow/lite/python:tflite_convert' depends on toolchain '#local_config_cc//:cc-compiler-darwin', which cannot be found: error loading package '#local_config_cc//': cannot load '#local_config_cc_toolchains//:osx_archs.bzl': no such file'
ERROR: Analysis of target '//tensorflow/tools/pip_package:build_pip_package' failed; build aborted: Analysis failed
When I try
pip3 install tensorflow-macos
I get this error:
Building wheel for h5py (pyproject.toml) ... error
ERROR: Command errored out with exit status 1:
command: /opt/homebrew/opt/python#3.9/bin/python3.9 /opt/homebrew/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /var/folders/gz/28jpdfcd3b3g4pm7zl0wmrkh0000gn/T/tmpz_m057zj
cwd: /private/var/folders/gz/28jpdfcd3b3g4pm7zl0wmrkh0000gn/T/pip-install-kz29fkw2/h5py_0747e63c821445b6944ecb4fc6b2d1e1
I'm basing my answer on the article from Prabhat Kumar Sahu:
How to install Tensorflow on M1 Mac the easy way
Set up environment
Make sure you have homebrew, xcode, and miniforge installed.
create a virtual environment
conda create --name mlp python=3.8
activate environment
conda activate mlp
Install tensorflow for mac-os
(sets up the wheel files etc.)
conda install -c apple tensorflow-deps
pip install tensorflow-macos
pip install tensorflow-metal
That's it. You should have the environment all ready to go. Look at Prabhat's article for a sample Jupyter Notebook test for an example of how to benchmark/test your environment.
Hey guys I had the same issue but I fixed it with the following instructions :
NOTE: If using conda environment built against pre-macOS 11 SDK use:
SYSTEM_VERSION_COMPAT=0 python -m pip install tensorflow-macos
otherwise, you will get errors like: “not a supported wheel on this platform”
STEPS :
OS Requirements macOS 12.0+ (latest beta)
Currently Not Supported
Multi-GPU support
Acceleration for Intel GPUs
V1 TensorFlow Networks
Installation Instructions
Step 1: Environment setup
CPU TYPE x86: AMD
Create virtual environment (recommended):
python3 -m venv ~/tensorflow-metal
source ~/tensorflow-metal/bin/activate
python -m pip install -U pip
NOTE: python version 3.8 required
CPU TYPE : arm64 : Apple Silicon
Download and install Conda env:
chmod +x ~/Downloads/Miniforge3-MacOSX-arm64.sh
sh ~/Downloads/Miniforge3-MacOSX-arm64.sh
source ~/miniforge3/bin/activate
OR
conda env create --file=environment.yml --name tf_m1
and then activate tf_m1
Install the TensorFlow dependencies:
conda install -c apple tensorflow-deps
When upgrading to new base TensorFlow version, we recommend:
uninstall existing tensorflow-macos and tensorflow-metal
python -m pip uninstall tensorflow-macos
python -m pip uninstall tensorflow-metal
Upgrade tensorflow-deps
conda install -c apple tensorflow-deps --force-reinstall
or point to specific conda environment
conda install -c apple tensorflow-deps --force-reinstall -n my_env
tensorflow-deps versions are following base TensorFlow versions so:
For v2.5:
conda install -c apple tensorflow-deps==2.5.0
For v2.6:
conda install -c apple tensorflow-deps==2.6.0
NOTE: Python versions 3.8 and 3.9 supported
Step 2: Install base TensorFlow
python -m pip install tensorflow-macos
NOTE: If using conda environment built against pre-macOS 11 SDK use:
SYSTEM_VERSION_COMPAT=0 python -m pip install tensorflow-macos
otherwise you will get errors like: “not a supported wheel on this
platform
Step 3: Install tensorflow-metal plugin
python -m pip install tensorflow-metal
The current default version of Python running on Google Colab is 3.7, but I need 3.9 for my notebooks to work.
How can I update Google Colab's Python version to 3.9 (or greater)?
In Google Colab you have a Debian-based Linux, and you can do whatever you can on a Debian Linux. Upgrading Python is as easy as upgrading it on your own Linux system.
Detect the current python version in Colab:
!python --version
#Python 3.8.16
Install new python version
Let's first install and upgrade to Python 3.9:
#install python 3.9
!sudo apt-get update -y
!sudo apt-get install python3.9
#change alternatives
!sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.8 1
!sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.9 2
#check python version
!python --version
#3.9.16
Port Colab kernel to the new installed python
As mentioned in the comments, the above commands just add a new python version to your google colab and update the default python for commandline usage. But your runtime packages such as sys are still running on the previous python version. The following commands need to be executed as well, to update the sys version.
# install pip for new python
!sudo apt-get install python3.9-distutils
!wget https://bootstrap.pypa.io/get-pip.py
!python get-pip.py
# credit of these last two commands blongs to #Erik
# install colab's dependencies
!python -m pip install ipython ipython_genutils ipykernel jupyter_console prompt_toolkit httplib2 astor
# link to the old google package
!ln -s /usr/local/lib/python3.8/dist-packages/google \
/usr/local/lib/python3.9/dist-packages/google
Now you can restart runtime and check the sys version. Note that in the new python version you have to install every packages, such as pandas, tensorflow, etc. from scratch.
Also, note that you can see a list of installed Python versions and switch between them at any time with this command:
(If nothing changed after installation, use this command to select python version manually)
!sudo update-alternatives --config python3
#after running, enter the row number of the python version you want.
It's also possible to update the kernel without going through ngrok or conda with some creative package installation.
Raha's answer suggesting making a link between the default google package and the newly installed Python version is the trick that makes this work because, at least with Python 3.9, the version of pandas (0.24.0) that the google package requires fails to build.
Here's the code I used to install and switch my Colab kernel to Python 3.9:
#install python 3.9 and dev utils
#you may not need all the dev libraries, but I haven't tested which aren't necessary.
!sudo apt-get update -y
!sudo apt-get install python3.9 python3.9-dev python3.9-distutils libpython3.9-dev
#change alternatives
!sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.8 1
!sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.9 2
#Check that it points at the right location
!python3 --version
# install pip
!curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
!python3 get-pip.py --force-reinstall
#install colab's dependencies
!python3 -m pip install ipython ipython_genutils ipykernel jupyter_console prompt_toolkit httplib2 astor
# link to the old google package
!ln -s /usr/local/lib/python3.8/dist-packages/google \
/usr/local/lib/python3.9/dist-packages/google
# There has got to be a better way to do this...but there's a bad import in some of the colab files
# IPython no longer exposes traitlets like this, it's a separate package now
!sed -i "s/from IPython.utils import traitlets as _traitlets/import traitlets as _traitlets/" /usr/local/lib/python3.9/dist-packages/google/colab/*.py
!sed -i "s/from IPython.utils import traitlets/import traitlets/" /usr/local/lib/python3.9/dist-packages/google/colab/*.py
If Google updates from Python 3.8, you'll have to change the path to the default package.
Then go the Runtime menu and select Restart runtime. It should reconnect and choose the updated version of Python as the default kernel. You can check that it worked with:
#check python version
import sys
print(sys.version)
!python3 --version
!python --version
To use another python version in google colab, you need to:
1- Installing Anaconda.
2- Adding (fake) google colab library.
3- Starting Jupyterlab.
4- Accessing it with ngrok.
# install Anaconda3
!wget -qO ac.sh https://repo.anaconda.com/archive/Anaconda3-2020.07-Linux-x86_64.sh
!bash ./ac.sh -b
# a fake google.colab library
!ln -s /usr/local/lib/python3.6/dist-packages/google \
/root/anaconda3/lib/python3.8/site-packages/google
# start jupyterlab, which now has Python3 = 3.8
!nohup /root/anaconda3/bin/jupyter-lab --ip=0.0.0.0&
# access through ngrok, click the link
!pip install pyngrok -q
from pyngrok import ngrok
print(ngrok.connect(8888))
you can also use:
# Install the python version
!apt-get install python3.9
# Select the version
!python3.9 setup.py
another way is to use a virtual environment with your desired python version:
virtualenv env --python=python3.9
Update 24.12.2022 - Unfortunately, the method does not work anymore.
This worked for me (copied from GitHub), I successfully installed Python 3.10.
#The code below installs 3.10 (assuming you now have 3.8) and restarts environment, so you can run your cells.
import sys #for version checker
import os #for restart routine
if '3.10' in sys.version:
print('You already have 3.10')
else:
#install python 3.10 and dev utils
#you may not need all the dev libraries, but I haven't tested which aren't necessary.
!sudo apt-get update -y
!sudo apt-get install python3.10 python3.10-dev python3.10-distutils libpython3.10-dev
!sudo apt-get install python3.10-venv binfmt-support #recommended in install logs of the command above
#change alternatives
!sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.8 1
!sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.10 2
# install pip
!curl -sS https://bootstrap.pypa.io/get-pip.py | python3.10
!python3 get-pip.py --force-reinstall
#install colab's dependencies
!python3 -m pip install setuptools ipython ipython_genutils ipykernel jupyter_console prompt_toolkit httplib2 astor
#minor cleanup
!sudo apt autoremove
#link to the old google package
!ln -s /usr/local/lib/python3.8/dist-packages/google /usr/local/lib/python3.10/dist-packages/google
#this is just to verify if 3.10 folder was indeed created
!ls /usr/local/lib/python3.10/
#restart environment so you don't have to do it manually
os.kill(os.getpid(), 9)
In addition to Kaveh's answer, I added the following code. (This colab python version is python 3.8 and I tried to downgrade to python 3.7)
!pip install google-colab==1.0.0
# install colab's dependencies
!python -m pip install ipython==7.9.0 ipython_genutils==0.2.0 ipykernel==5.3.4 jupyter_console==6.1.0 prompt_toolkit==2.0.10 httplib2==0.17.4 astor==0.8.1 traitlets==5.7.1 google==2.0.3
This way, I solved the crashing runtime error.
Simple as that: -
!wget -O mini.sh https://repo.anaconda.com/miniconda/Miniconda3-py39_4.9.2-Linux-x86_64.sh
!chmod +x mini.sh
!bash ./mini.sh -b -f -p /usr/local
!conda install -q -y jupyter
!conda install -q -y google-colab -c conda-forge
!python -m ipykernel install --name "py39" --user
Source: https://colab.research.google.com/drive/1m47aWKayWTwqJG--x94zJMXolCEcfyPS?usp=sharing#scrollTo=r3sLiMIs8If3
I installed Tensorflow-macos and try to install opencv-python
but always fail in this message
ERROR: Command errored out with exit status 1: /Users/sean/Documents/sysvenv/tf24v/bin/python3 /Users/sean/Documents/sysvenv/tf24v/lib/python3.8/site-packages/pip install --ignore-installed --no-user --prefix /private/var/folders/gy/jzs3xnwd1z3203d75y_31nxc0000gn/T/pip-build-env-en64krht/overlay --no-warn-script-location -v --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel scikit-build cmake pip 'numpy==1.13.3; python_version=='"'"'3.6'"'"'' 'numpy==1.14.5; python_version=='"'"'3.7'"'"'' 'numpy==1.17.3; python_version=='"'"'3.8'"'"'' 'numpy==1.19.3; python_version>='"'"'3.9'"'"'' Check the logs for full command output.
it lookalike the bumpy version problem.
But In Tensorflow-macos it it 1.8.5 and python is 3.8
Does anynoe have the same problem?
thanks
You might want to look at these suggestions:
opencv issues with M1 MAC - OpenCV imshow doesnot work
conda install opencv
I was successful in installing Python 3.9.1 for Apple Silicon and then running conda install opencv. However, the slow time to compute a few functions for the first time might suggest some components are still being translated via Rosetta. Regardless, while I did not test performance the functions I needed seemed to work.
after searching the web I have successfully installed OpenCV on my Mac M1.
Probably you don't have brew installed, so here's how you should install it:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
brew install wget
brew install miniforge
brew install cmake, you will need cmake for building OpenCV code
Then just follow this blog: https://sayak.dev/install-opencv-m1/#Install-conda
OR, here is the YouTube video which explains the second step: https://youtu.be/x_kAkabk-5o
P.S. If mdfind cv2.cpython returning an empty string then try to delete the build folder and compile opencv again. Otherwise, you have done everything correctly.
I am trying to run this statement in MacOS.
conda install -c conda-forge tensorflow
It just stuck at the
Solving Environment:
Never finish.
$ conda --version
conda 4.5.12
Nothing worked untill i ran this in conda terminal:
conda upgrade conda
Note that this was for poppler (conda install -c conda-forge poppler)
On win10 I waited about 5-6 minutes but it depends of the number of installed python packages and your internet connection.
Also you can install it via Anaconda Navigator
One can also resolve the "Solving environment" issue by using the mamba package manager.
I installed tensorflow-gpu==2.6.2 on Linux (CentOS Stream 8) using the following commands
conda create --name deeplearning python=3.8
conda activate deeplearning
conda install -c conda-forge mamba
mamba install -c conda-forge tensorflow-gpu
To check the successful usage of GPU, simply run either of the commands
python -c "import tensorflow as tf;print('\n\n\n====================== \n GPU Devices: ',tf.config.list_physical_devices('GPU'), '\n======================')"
python -c "import tensorflow as tf;print('\n\n\n====================== \n', tf.reduce_sum(tf.random.normal([1000, 1000])), '\n======================' )"
References
Conda Forge blog post
mamba install instead of conda install
The same error happens with me .I've tried to install tensorboard with anaconda prompt but it was stuck on the environment solving .So i've added these paths to my environment variables:
C:\Anaconda3
C:\Anaconda3\Library\mingw-w64\bin
C:\Anaconda3\Library\usr\bin
C:\Anaconda3\Library\bin
C:\Anaconda3\Scripts
and it worked well.
Follow the instruction by nekomatic.
I left it running for 1 hour. Yes. it is finally finished.
But now I got the conflicts
Solving environment: failed
UnsatisfiableError: The following specifications were found to be in conflict:
- anaconda==2018.12=py37_0 -> bleach==3.0.2=py37_0
- anaconda==2018.12=py37_0 -> html5lib==1.0.1=py37_0
- anaconda==2018.12=py37_0 -> numexpr==2.6.8=py37h7413580_0
- anaconda==2018.12=py37_0 -> scikit-learn==0.20.1=py37h27c97d8_0
- tensorflow
Use "conda info <package>" to see the dependencies for each package.
I installed the latest Tensorflow 0.5.0 from source via git clone.
and want to update to Tensorflow 0.6.0
git pull
./configure
bazel build -c opt --config=cuda //tensorflow/cc:tutorials_example_trainer
but the Tensorflow library in the directory /usr/lib/python2.7/site-packages still has the version 0.5.0
the version in the result of "pip show tensorflow" also is 0.5.0
To install the TensorFlow library from source, you need to build a PIP package and install it. The steps are as follows:
$ git pull
$ ./configure
$ bazel build -c opt //tensorflow/tools/pip_package:build_pip_package
# ...or, with GPU support
$ bazel build -c opt --config=cuda //tensorflow/tools/pip_package:build_pip_package
$ bazel-bin/tensorflow/tools/pip_package/build_pip_package /tmp/tensorflow_pkg
# The name of the .whl file will depend on your platform.
$ pip install /tmp/tensorflow_pkg/tensorflow-0.6.0-cp27-none-linux_x86_64.whl
git pull doesn't work for me since some local files are modified by the last build so with a slight modification I update like this:
git fetch --all
git reset --hard origin/master
./configure
bazel build -c opt --config=cuda //tensorflow/tools/pip_package:build_pip_package
bazel-bin/tensorflow/tools/pip_package/build_pip_package /tmp/tensorflow_pkg
sudo pip install /tmp/tensorflow_pkg/tensorflow-0.8.0-py2-none-any.whl
Tested to work as of today. The Installation from Source instructions in tensorflow docs are misleading in the sense they only include the real pip wheel installation commands for Mac and the example-trainer build command exists instead in Linux instructions.
To show the version:
python -c "import tensorflow; print(tensorflow.__version__);"
And if it is not the latest, you have uninstall it via pip uninstall:
sudo pip uninstall tensorflow
and subsequently install it:
export TF_BINARY_URL=https://storage.googleapis.com/tensorflow/linux/gpu/tensorflow-0.9.0-cp27-none-linux_x86_64.whl
sudo pip install $TF_BINARY_URL
Before trying to update tensorflow try updating pip
pip install --upgrade pip
If you are upgrading from a previous installation of TensorFlow < 0.7.1, you should uninstall the previous TensorFlow and protobuf using,
pip uninstall
first to make sure you get a clean installation of the updated protobuf dependency.
Uninstall the TensorFlow on your system, and check out Download and Setup to reinstall again.
If you are using pip install, go check the available version over https://storage.googleapis.com/tensorflow, search keywords with linux/cpu/tensorflow to see the availabilities.
Then, set the path for download and execute in sudo.
$ export TF_BINARY_URL=https://storage.googleapis.com/tensorflow/linux/cpu/tensorflow-1.0.0-py2-none-any.whl
$ sudo pip install --upgrade $TF_BINARY_URL
For more detail, follow this link in here
If you get the error saying not a supported wheel on this platform. You might be updating tensorflow for python3. For that you will need pip3
Try installing pip3
sudo apt-get -y install python3-pip
Then, set the path for download if you haven't already set the path
$ export TF_BINARY_URL=https://storage.googleapis.com/tensorflow/linux/cpu/tensorflow-1.1.0rc0-cp35-cp35m-linux_x86_64.whl
$ pip3 install --ignore-installed --upgrade $TF_BINARY_URL
updating tensorflow install with sudo pip install --upgrade https://storage.googleapis.com/tensorflow/linux/cpu/tensorflow-0.7.1-cp27-none-linux_x86_64.whl.
I find it in the below issue,mohamed-ali's comment. https://github.com/tensorflow/tensorflow/issues/1105