I have tried to install qiime2 using ubuntu and anaconda many many times , in ubuntu it gives me following problem everytime I tried to do it
whereas when I tried anaconda it says wget does not found even when I try to instal wget using commands I failed
Welcome to the forum, @sadaffaheem.
In the future, please remove the template copy when you post - it makes it harder for us to find your question within the topic. I took care of it for you here.
You've got a few different questions here, but have only provided details for one of them. I'll try to help with that, and we'll explore other options as needed. It looks like your computer is able to connect to data.qiime2.org
but not to raw.github.usercontent.com
I searched the forum 
for "connection refused", and found many helpful results. This is often the result of institutional or national firewalls. Try navigating to the github URL with your browser to download directly. If that doesn't work, contact your network administrator. They may be able to help you connect.
Let us know how it goes!
some friend helped me to download it directly but even that one does not worked, I do not know why. can it be due to network as I am doing it in a university in
China
Github is frequently a target of China's "great firewall", and may be blocked by local networks as well, so that doesn't surprise me. If you'd care to share the error messages you got while trying to install from the file your friend shared, maybe we can troubleshoot?
ok, let me share the error with that file , as I do not know who to share so I am copy pasting all
(base) sadaffaheem@DESKTOP-BI1UVNU:~$ conda env create -n qiime2-2021.4 --file qiime2-2021.4-py38-linux-conda.yml
Traceback (most recent call last):
File "/home/sadaffaheem/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1079, in __call__
return func(*args, **kwargs)
File "/home/sadaffaheem/anaconda3/lib/python3.8/site-packages/conda_env/cli/main.py", line 80, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/home/sadaffaheem/anaconda3/lib/python3.8/site-packages/conda_env/cli/main_create.py", line 81, in execute
spec = specs.detect(name=name, filename=get_filename(args.file), directory=os.getcwd())
File "/home/sadaffaheem/anaconda3/lib/python3.8/site-packages/conda_env/specs/__init__.py", line 43, in detect
if spec.can_handle():
File "/home/sadaffaheem/anaconda3/lib/python3.8/site-packages/conda_env/specs/yaml_file.py", line 18, in can_handle
self._environment = env.from_file(self.filename)
File "/home/sadaffaheem/anaconda3/lib/python3.8/site-packages/conda_env/env.py", line 159, in from_file
with open(filename, 'rb') as fp:
PermissionError: [Errno 13] Permission denied: '/home/sadaffaheem/qiime2-2021.4-py38-linux-conda.yml'
$ /home/sadaffaheem/anaconda3/bin/conda-env create -n qiime2-2021.4 --file qiime2-2021.4-py38-linux-conda.yml
environment variables:
CIO_TEST=
CONDA_AUTO_UPDATE_CONDA=false
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/sadaffaheem/anaconda3/bin/conda
CONDA_PREFIX=/home/sadaffaheem/anaconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/home/sadaffaheem/anaconda3/bin/python
CONDA_ROOT=/home/sadaffaheem/anaconda3
CONDA_SHLVL=1
CURL_CA_BUNDLE=
PATH=/home/sadaffaheem/anaconda3/bin:/home/sadaffaheem/anaconda3/bin:/home/
sadaffaheem/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbi
n:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/mnt/c/Program Files
/WindowsApps/CanonicalGroupLimited.Ubuntu20.04onWindows_2004.2021.222.
0_x64__79rhkp1fndgsc:/mnt/c/Python/Python395/Scripts:/mnt/c/Python/Pyt
hon395:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/
Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0:/mnt/c/WINDOWS/Sys
tem32/OpenSSH:/mnt/c/Program Files (x86)/IVI
Foundation/VISA/WinNT/Bin:/mnt/c/Program Files/IVI
Foundation/VISA/Win64/Bin:/mnt/c/Program Files (x86)/IVI Foundation/VI
SA/WinNT/Bin:/mnt/c/Users/admin/AppData/Local/Microsoft/WindowsApps:/m
nt/c/Program Files/Bandizip:/snap/bin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
active environment : base
active env location : /home/sadaffaheem/anaconda3
shell level : 1
user config file : /home/sadaffaheem/.condarc
populated config files :
conda version : 4.10.1
conda-build version : 3.21.4
python version : 3.8.8.final.0
virtual packages : __linux=4.4.0=0
__glibc=2.31=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/sadaffaheem/anaconda3 (writable)
conda av data dir : /home/sadaffaheem/anaconda3/etc/conda
conda av metadata url : main
channel URLs : main/linux-64
main/noarch
r/linux-64
r/noarch
package cache : /home/sadaffaheem/anaconda3/pkgs
/home/sadaffaheem/.conda/pkgs
envs directories : /home/sadaffaheem/anaconda3/envs
/home/sadaffaheem/.conda/envs
platform : linux-64
user-agent : conda/4.10.1 requests/2.25.1 CPython/3.8.8 Linux/4.4.0-19041-Microsoft ubuntu/20.04.2 glibc/2.31
UID:GID : 1000:1000
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers?
[y/N]:
A few questions:
/home/sadafffaheem/ and then run ls -lah, what do the permissions look like for qiime2-2021.4-py38-linux-conda.yml?for anaconda prompt, it gives this error
(base) C:\WINDOWS\system32>conda env create -n qiime2-2021.4 --file qiime2-2021.4-py38-linux-conda.yml
SpecNotFound: Invalid name, try the format: user/package
(base) C:\WINDOWS\system32>anaconda-navigator
'anaconda-navigator' is not recognized as an internal or external command,
operable program or batch file.
(base) C:\WINDOWS\system32>anaconda navigator
'anaconda' is not recognized as an internal or external command,
operable program or batch file.
(base) C:\WINDOWS\system32>conda install -y wget
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:
- wget
Current channels:
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/win-64
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/noarch
- https://repo.anaconda.com/pkgs/main/win-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/win-64
- https://repo.anaconda.com/pkgs/r/noarch
- https://repo.anaconda.com/pkgs/msys2/win-64
- https://repo.anaconda.com/pkgs/msys2/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
I also have ubuntu installed as shown by a video on youtube by some person who showed to install it
I think it is not root access, it is university administration controlling it
Please use triple-backticks to display copy-pasted code as code blocks - it makes it much clearer what's going on. I've edited the post above for you as an example.
qiime2-2021.4-py38-linux-conda.yml file.The r w and x characters on the left side of this guy tell you who has read, write, and execute access to those files.
It's unusual to see --------, because it means nobody has permission to do anything with that file. I suspect this might be a WSL2/Linux thing.
Try navigating back to the directory in which you ran the ls command, and running chmod 744 qiime2-2021.4-py38-linux-conda.yml. Re-run the ls -lah command to confirm the permissions for that file are no longer --------, and then try creating the environment again with conda. Let us know how it goes.
I'd strongly encourage you to spend some time reading up on how unix-like systems work. That may sound imposing at first, but there are tons of good tutorials out there. This one does a nice job covering file permissions, and will give you clearer picture of what the notation and commands above mean.
wowwwwwwwwwwwww, it worked for me, after 3 weeks at last I did it, thank you so much for your time and support, I am really very very thankful. you resolved a big problem for me
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