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Downloading blat to M1 mac

I am trying to download the blat package so that I can use the GAMMA program to analyze mutations in some sequences. I have bioconda install and I am using one-liner code to download blat described here: https://shanguangyu.com/articles/install-blat-on-mac-with-one-liner-command/
I think the issue could be that blat is not made for M1 macs. I previously had it installed on an older mac but I don't remember how I did that. I am a beginner/proficient coder so it could be an obvious error. Any help is appreciated.
Here is my code:
conda install -c bioconda blat
Here is my error:
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- blat
Current channels:
- https://conda.anaconda.org/bioconda/osx-arm64
- https://conda.anaconda.org/bioconda/noarch
- https://conda.anaconda.org/conda-forge/osx-arm64
- https://conda.anaconda.org/conda-forge/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org

You got to the root of the issue. M1 Macs use an ARM64-based architecture as opposed to x64. The website for blat does not list ARM compatibility, and, addressing the M1 specifically, a quick examination of the last update to the files shows that they predate the launch of the Apple Silicon Macs, just like the website you got the command from. Anaconda itself added support for ARM64 only recently. x64 translation does exist for macOS apps, but I don't think I've heard of one for blat.

From post update
This seems to be a common issue for Python users on new M1 macs. Many python packages are not made for ARM chips
This is solved by downloading homebrew and miniforge and using this code:
CONDA_SUBDIR=osx-64 conda create -n [environment] # create a new environment
conda activate [environment]
conda env config vars set CONDA_SUBDIR=osx-64 # subsequent commands use intel packages
https://naolin.medium.com/conda-on-m1-mac-with-miniforge-bbc4e3924f2b
https://towardsdatascience.com/using-conda-on-an-m1-mac-b2df5608a141
https://github.com/Haydnspass/miniforge#rosetta-on-mac-with-apple-silicon-hardware

Anaconda, and Pycharm set up. Error on Manjaro KDE

So I have been encountering some problems with setting up a proper Anaconda Interpreter with Pycharm. Per the documentation on the anaconda website, and the Pycharm website they are suggesting that I go to the Add Interpreter settings near the bottom right of the Pycharm GUI, once I click on the current interpreter.
For example,Pycharm is saying my current interpreter is Python 3.9 . Then click on the Conda Environment which I did, however, when I have done so I am getting an Error Message like:
CondaError: Unable to create prefix directory '/opt/anaconda/envs/pythonProject9'.
Here is the command output as well:
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /opt/anaconda/envs/pythonProject9
added / updated specs:
- python=3.9
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
ca-certificates pkgs/main/linux-64::ca-certificates-2021.4.13-h06a4308_1
certifi pkgs/main/linux-64::certifi-2020.12.5-py39h06a4308_0
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2
libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
ncurses pkgs/main/linux-64::ncurses-6.2-he6710b0_1
openssl pkgs/main/linux-64::openssl-1.1.1k-h27cfd23_0
pip pkgs/main/linux-64::pip-21.0.1-py39h06a4308_0
python pkgs/main/linux-64::python-3.9.4-hdb3f193_0
readline pkgs/main/linux-64::readline-8.1-h27cfd23_0
setuptools pkgs/main/linux-64::setuptools-52.0.0-py39h06a4308_0
sqlite pkgs/main/linux-64::sqlite-3.35.4-hdfb4753_0
tk pkgs/main/linux-64::tk-8.6.10-hbc83047_0
tzdata pkgs/main/noarch::tzdata-2020f-h52ac0ba_0
wheel pkgs/main/noarch::wheel-0.36.2-pyhd3eb1b0_0
xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3
Preparing transaction: ...working... failed
==> WARNING: A newer version of conda exists. <==
current version: 4.9.2
latest version: 4.10.1
Please update conda by running
$ conda update -n base -c defaults conda
Is there something that I am doing wrong? Does anyone need pictures for the PATH? I am not certain if my problem is similar to another individual on here who asked a similar question. My Pycharm IDE is update for what its worth.

The error (which you should have copy-pasted, not screenshotted) says
Unable to create prefix directory /opt/anaconda/envs/pythonProject9
Check you have sufficient permissions.
My best guess is that you've installed Anaconda as root (e.g. using sudo) and are using PyCharm as a regular user (as you should).
If possible, tell PyCharm (or Anaconda) to use a different base path for the environment it's attempting to create, e.g. one under your home directory, or if you're feeling daring, you might chmod /opt/anaconda/envs so you, too, can write there.

Facing issue while installing fancyimpute

For installing the fancyimpute, i am using the below commands:
conda install ecos
conda install CVXcanon
pip install fancyimpute
On firing the 1st command "conda install ecos", i am getting the below error. Please help me on this resolution.
Preparing transaction: done
Verifying transaction: done
Executing transaction: | DEBUG menuinst_win32:__init__(196): Menu: name: 'Anaconda${PY_VER} ${PLATFORM}', prefix: 'C:\Users\Deepak\Anaconda3', env_name: 'None', mode: 'user', used_mode: 'user'
DEBUG menuinst_win32:create(320): Shortcut cmd is C:\Users\Deepak\Anaconda3\pythonw.exe, args are ['C:\\Users\\Deepak\\Anaconda3\\cwp.py', 'C:\\Users\\Deepak\\Anaconda3', 'C:\\Users\\Deepak\\Anaconda3\\pythonw.exe', 'C:\\Users\\Deepak\\Anaconda3\\Scripts\\spyder-script.py']
/ DEBUG menuinst_win32:create(320): Shortcut cmd is C:\Users\Deepak\Anaconda3\python.exe, args are ['C:\\Users\\Deepak\\Anaconda3\\cwp.py', 'C:\\Users\\Deepak\\Anaconda3', 'C:\\Users\\Deepak\\Anaconda3\\python.exe', 'C:\\Users\\Deepak\\Anaconda3\\Scripts\\spyder-script.py', '--reset']
failed
ERROR conda.core.link:_execute(502): An error occurred while installing package 'conda-forge::automat-0.7.0-py_1'.
CondaError: Cannot link a source that does not exist. C:\Users\Deepak\Anaconda3\Scripts\conda.exe
Running `conda clean --packages` may resolve your problem.
Attempting to roll back.
Rolling back transaction: done
CondaError: Cannot link a source that does not exist. C:\Users\Deepak\Anaconda3\Scripts\conda.exe
Running `conda clean --packages` may resolve your problem.
Note: Tried the same command after using "conda clean --packages". But still the issue persists.
Regards,
Deepak

According to this GitHub issue about the same problem (transaction also fails on automat), there are a few things that seem to get it working:
Cleaning. You've already tried conda clean --packages, so maybe you can ignore this one, but the thread also suggests conda clean --all. Personally, I think that's a bit blunt. The users who it worked for may have only needed --packages.
Update Conda. Many seem to get around this by updating Conda, conda update -n base conda.
Update Anaconda. Some said it worked to run conda update anaconda.
Freeze installed packages. Some users noticed that it only happens when planned transactions include updating other packages. One can prevent other packages from updating by using conda install --freeze-installed ecos.
Issue with latest Automat. One user reports the issue is specific to the recent 0.7.0 version of Automat. They report having a successful transaction by explicitly requesting the previous Automat version, e.g., conda install ecos automat=0.6.*
Recommendation
I would try (2) first.
Something I find strange in all this is that everyone reporting this is on Windows, but Conda attempts to install the noarch version (as indicated by the py_1 in the tarball). Nothing particularly wrong with that, but on OSX, Conda specifically tries to install the osx-64 version. Hence, I would attempt to explicitly install the win-64 version of 0.7.0 and see if that works. That is,
conda install conda-forge/win-64::automat
If that doesn't work, I suppose I would try (4) or (5) next.

Install ROS Kinetic on MacOS under a separate Anaconda environment

I'm installing ROS Kinetic on MacOS Sierra 10.12.6 under a seperate environment under Python Anaconda distribution.
Here is my python version(my seperate python environment in Anaconda is called "ros-kinetic"):
(ros-kinetic) jizhe#jizhedeMacBook-Pro  ~/ros_catkin_ws  python --version
Python 3.6.4 :: Anaconda, Inc.
I followed the guide: http://wiki.ros.org/kinetic/Installation/OSX/Homebrew/Source.
When I execute the "rosdep install" command, I got the following error:
(ros-kinetic) jizhe#jizhedeMacBook-Pro ~/ros_catkin_ws  rosdep install --from-paths src --ignore-src --rosdistro kinetic -y
ERROR: the following packages/stacks could not have their rosdep keys resolved
to system dependencies:
actionlib: No definition of [python-wxtools] for OS [osx]
catkin: No definition of [google-mock] for OS [osx]
roslisp: No definition of [google-mock] for OS [osx]
Obviously, there is something wrong with the package "python-wxtools" and "google-mock".
I've already install the wxpython via "brew install wxpython", and here is the wxpython info:
(ros-kinetic) jizhe#jizhedeMacBook-Pro  ~/ros_catkin_ws  brew info wxpython
wxpython: stable 3.0.2.0 (bottled)
Python bindings for wxWidgets
https://www.wxwidgets.org/
/usr/local/Cellar/wxpython/3.0.2.0_1 (1,108 files, 37.9MB) *
Poured from bottle on 2018-02-24 at 03:56:21
From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/wxpython.rb
==> Dependencies
Required: wxmac ✔
==> Caveats
Python modules have been installed and Homebrew's site-packages is not
in your Python sys.path, so you will not be able to import the modules
this formula installed. If you plan to develop with these modules,
please run:
mkdir -p /Users/jizhe/Library/Python/2.7/lib/python/site-packages
echo 'import site; site.addsitedir("/usr/local/lib/python2.7/site-packages")' >> /Users/jizhe/Library/Python/2.7/lib/python/site-packages/homebrew.pth
And I've already run the command:
$ mkdir -p ~/Library/Python/2.7/lib/python/site-packages
$ echo "$(brew --prefix)/lib/python2.7/site-packages" >> ~/Library/Python/2.7/lib/python/site-packages/homebrew.pth
So, what's wrong with the package "google-mock" and "python-wxtools", how can I solve this problem?

Try installing with --skip-keys python-wxtools --skip-keys google-mock. It worked for me.

There is a ticket for this issue. Basically the workaround is to install googletest manually. Not sure what's wrong with python-wxtools.
edit: If you're using ros-install-osx, you can add the following lines to your rosdeps.yaml file:
google-mock:
osx:
homebrew:
packages: []

I found this question from a Google search, just for your information in 2021 installing ROS in conda also on macOS should be much straightforward, see the following links:
https://medium.com/robostack/cross-platform-conda-packages-for-ros-fa1974fd1de3
https://github.com/RoboStack/ros-noetic

XGBoostLibraryNotFound: Cannot find XGBoost Library in the candidate path, did you install compilers and run build.sh in root path?

I am facing this problem while moving the python-package directory of XGBoost.
Traceback (most recent call last): File "setup.py", line 19, in LIB_PATH = libpath'find_lib_path' File "xgboost/libpath.py", line 46, in find_lib_path 'List of candidates:\n' + ('\n'.join(dll_path))) builtin.XGBoostLibraryNotFound: Cannot find XGBoost Library in the candidate path, did you install compilers and run build.sh in root path?
Could anyone explain to me how to fix it?
thanks in advance.

You get that message when trying to install the xgboost Python package without the xgboost binaries present. The proper way to install the xgboost Python package from source is the following (assuming you have a compiler such as gcc installed):
git clone --recursive https://github.com/dmlc/xgboost.git
cd xgboost
./build.sh
cd python-package
python setup.py install
I prefer to do it inside a virtual environment. Note that the option --recursive when cloning the repo is essential since it will also clone folders from different repos such as dmlc-core which are necessary for building xgboost.

The other answers didn't work for me so I installed xgboost through Conda commands as listed here.
Just run conda install -c conda-forge xgboost

The first answer's suggestions did not work for me, and left me with the same error as the original question.
If I'm assuming correctly that your full error message is something like this:
C:\Users\Matt\xgboost\python-package>python setup.py install
Traceback (most recent call last):
File "setup.py", line 19, in <module>
LIB_PATH = [os.path.relpath(libfile, CURRENT_DIR) for libfile in libpath['find_lib_path']()]
File "xgboost/libpath.py", line 49, in find_lib_path
'List of candidates:\n' + ('\n'.join(dll_path)))
XGBoostLibraryNotFound: Cannot find XGBoost Library in the candidate path, did you install compilers and run build.sh in root path?
List of candidates:
C:\Users\Matt\xgboost\python-package\xgboost\xgboost.dll
C:\Users\Matt\xgboost\python-package\xgboost\../../lib/xgboost.dll
C:\Users\Matt\xgboost\python-package\xgboost\./lib/xgboost.dll
C:\Users\Matt\AppData\Local\Programs\Python\Python35\xgboost\xgboost.dll
C:\Users\Matt\xgboost\python-package\xgboost\../../windows/x64/Release/xgboost.dll
C:\Users\Matt\xgboost\python-package\xgboost\./windows/x64/Release/xgboost.dll
then the solution is to
1) Get/find/download the library that setup.py is looking for. Search the xgboost folder for .dll files. See if you can find something like xgboost.dll it might be called libxgboost.dll. If you can, move to step 2. If you cannot find it download it here
2) Copy the .dll file into the xgboost/python-package/xgboost folder. If that .dll is not called xgboost.dll (i.e. if it's called libxgboost.dll) then change the name to xgboost.dll
3) Run the commands as outlined in Gustavo answer. Note these are meant to be run from Git Bash.
If you want a more soup-to-nuts tutorial, this was the best one I found.

thanks to Joe Nyland that found the a good answer for this problem in here.
As he said (and also worked for me) you need to run following commands:
$ brew install gcc#5
$ pip install xgboost

Try this it worked for me:
brew install gcc-5
brew install cmake
pip install xgboost

In my case (Ubuntu 16.04, with CUDA 9.0) the Python library build was evidently broken by adding R library package to the cmake options list:
1) python lib installation works OK:
cmake .. -DUSE_CUDA=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-${CUDA_VER}
cd /tmp/xgboost/python-package && python3 setup.py install
2) adding '-DR_LIB=ON' switch to cmake breaks subsequent python library installation attempt:
cmake .. -DUSE_CUDA=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-${CUDA_VER} -DR_LIB=ON
cd /tmp/xgboost/python-package && python3 setup.py install
> "XGBoostLibraryNotFound: Cannot find XGBoost Library in the candidate path, did you install compilers and run build.sh in root
> path?"

I had the same issues. I downloaded the file (xgboost.dll) from
(https://picnet.com.au/blog/xgboost-windows-x64-binaries-for-download/)
into the already existing xgboost folder
(C:\Users\Naganandini\AppData\Roaming\Python\Python37\site-packages\xgboost).
It's perfectly working now :)

I faced the same error while installing xgboost using anaconda prompt because the installation of xgboost was interfering with the versions of some other pre-installed libraries. Installing xgboost by creating a virtual environment solved the issue.
On macOS and Linux:
python3 -m pip install --user virtualenv #Install virtualenv module
python3 -m venv env #Create a virtual environment 'env'
source env/bin/activate #Activate virtual environment
pip install xgboost #Install xgboost
On Windows:
py -m pip install --user virtualenv #Install virtualenv module
py -m venv env #Create a virtual environment 'env'
.\env\Scripts\activate #Activate virtual environment
pip install xgboost #Install xgboost
Refer https://packaging.python.org/guides/installing-using-pip-and-virtual-environments for help regarding virtual environment.

Search for xgboost.dll file under your C:\Users<your-user-name> directory.
If you have installed xgboost, somewhere you should find a copy of the xgboost.dll file.
Once you find the xgboost.dll file, just copy it to one of the paths mentioned in the error message,
e.g. C:\Users<your-user-name>\AppData\Roaming\Python\Python37\site-packages\xgboost\ . Import should work now.

1.I started off with the conda installation from anaconda prompt:
(base) C:\Users\abhi.b>conda install -c anaconda py-xgboost
This lead to the following error :
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: \
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.|
failed
UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
Specifications:
- py-xgboost -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
Your python: python=3.8
If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.
Decided not to followup this path, as exploring python downgrade was not an option for me.
2.There after i followed "The final attempt that works " on the below link :
https://medium.com/analytics-vidhya/this-is-what-you-should-do-if-you-fail-to-install-the-latest-or-an-older-version-of-xgboost-on-7942a7641eee
However i got the same error as other users faced ::
>>> import xgboost as xgb
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Users\abhi.b\Anaconda3\lib\site-packages\xgboost\__init__.py", line 11, in <module>
from .core import DMatrix, Booster
File "C:\Users\abhi.b\Anaconda3\lib\site-packages\xgboost\core.py", line 161, in <module>
_LIB = _load_lib()
File "C:\Users\abhi.b\Anaconda3\lib\site-packages\xgboost\core.py", line 123, in _load_lib
lib_paths = find_lib_path()
File "C:\Users\abhi.b\Anaconda3\lib\site-packages\xgboost\libpath.py", line 45, in find_lib_path
raise XGBoostLibraryNotFound(
xgboost.libpath.XGBoostLibraryNotFound: Cannot find XGBoost Library in the candidate path, did you install compilers and run build.sh in root path?
List of candidates:
C:\Users\abhi.b\Anaconda3\lib\site-packages\xgboost\xgboost.dll
C:\Users\abhi.b\Anaconda3\lib\site-packages\xgboost\../../lib/xgboost.dll
C:\Users\abhi.b\Anaconda3\lib\site-packages\xgboost\./lib/xgboost.dll
C:\Users\abhi.b\Anaconda3\xgboost\xgboost.dll
C:\Users\abhi.b\Anaconda3\lib\site-packages\xgboost\../../windows/x64/Release/xgboost.dll
C:\Users\abhi.b\Anaconda3\lib\site-packages\xgboost\./windows/x64/Release/xgboost.dll
>>> exit()
BTW the link to download xgboost.dll as posted above -
https://picnet.com.au/blog/xgboost-windows-x64-binaries-for-download/
was not clear to me ,so i decided to not follow this thread.
3.Finally ,the solution was very simple for me,Open ANACONDA PROMPT and Type
(base) C:\Users\abhi.b>pip install xgboost
This lead to
Collecting xgboost
Downloading xgboost-1.2.1-py3-none-win_amd64.whl (86.5 MB)
|████████████████████████████████| 86.5 MB 1.7 MB/s
Requirement already satisfied: scipy in c:\users\abhi.b\anaconda3\lib\site-packages (from xgboost) (1.5.0)
Requirement already satisfied: numpy in c:\users\abhi.b\anaconda3\lib\site-packages (from xgboost) (1.18.5)
Installing collected packages: xgboost
Successfully installed xgboost-1.2.1
Then goto python prompt
(base) C:\Users\abhi.b>python
>>>import xgboost as xgb
Or you can type the same command on IDE ie Spyder etc
Voila!!