Dear everyone,
I have tried to follow the protocol of dx-toolkit upgrade as described in following link: Downloads - DNAnexus Documentation. However, I get following error:
PS C:\WINDOWS\system32> dx upgrade
Upgrading to v0.332.0
Traceback (most recent call last):
File "C:\Program Files (x86)\DNAnexus CLI\python27\Lib\site-packages\dxpy\scripts\dx.py", line 3787, in upgrade
os.execv(cmd, args.args)
OSError: [Errno 2] No such file or directory
I am using Windows 10 and have Python 3.1 installed. I suspect though that Python 2.7 interferes with the upgrade. Do any of you have a suggestion for how to solve the issue?
Best,
Steffan
Requirement already satisfied: dxpy in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (0.332.0)
Requirement already satisfied: websocket-client==0.54.0 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from dxpy) (0.54.0)
Requirement already satisfied: python-dateutil>=2.5 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from dxpy) (2.8.2)
Requirement already satisfied: psutil>=3.3.0 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from dxpy) (5.9.1)
Requirement already satisfied: requests<=2.27.1,>=2.8.0 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from dxpy) (2.27.1)
Requirement already satisfied: cryptography<37,>=3.4.2 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from dxpy) (36.0.2)
Requirement already satisfied: argcomplete>=2.0.0 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from dxpy) (2.0.0)
Requirement already satisfied: colorama==0.4.4 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from dxpy) (0.4.4)
Requirement already satisfied: pyreadline3==3.4.1 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from dxpy) (3.4.1)
Requirement already satisfied: six in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from websocket-client==0.54.0->dxpy) (1.16.0)
Requirement already satisfied: cffi>=1.12 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from cryptography<37,>=3.4.2->dxpy) (1.15.1)
Requirement already satisfied: charset-normalizer~=2.0.0 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from requests<=2.27.1,>=2.8.0->dxpy) (2.0.12)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from requests<=2.27.1,>=2.8.0->dxpy) (1.26.11)
Requirement already satisfied: certifi>=2017.4.17 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from requests<=2.27.1,>=2.8.0->dxpy) (2022.6.15)
Requirement already satisfied: idna<4,>=2.5 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from requests<=2.27.1,>=2.8.0->dxpy) (3.3)
Requirement already satisfied: pycparser in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from cffi>=1.12->cryptography<37,>=3.4.2->dxpy) (2.21)
The folders seem to be added to following path "C:\Program Files (x86)\DNAnexus CLI\python27\Lib\site-packages" (see below) but when I use DNAnexus CLI, dx-toolkit still runs as v0.325.1.
Comments
5 comments
Do you remember how you installed dx-toolkit?
I would be interested what happens if you try to update it via "pip3 install --upgrade dxpy"...?
I think I used the .exe (https://dnanexus-sdk.s3.amazonaws.com/dx-toolkit-v0.325.1.exe) from Downloads - DNAnexus Documentation.
C:\WINDOWS\system32>pip3 install --upgrade dxpy
Requirement already satisfied: dxpy in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (0.332.0)
Requirement already satisfied: websocket-client==0.54.0 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from dxpy) (0.54.0)
Requirement already satisfied: python-dateutil>=2.5 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from dxpy) (2.8.2)
Requirement already satisfied: psutil>=3.3.0 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from dxpy) (5.9.1)
Requirement already satisfied: requests<=2.27.1,>=2.8.0 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from dxpy) (2.27.1)
Requirement already satisfied: cryptography<37,>=3.4.2 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from dxpy) (36.0.2)
Requirement already satisfied: argcomplete>=2.0.0 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from dxpy) (2.0.0)
Requirement already satisfied: colorama==0.4.4 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from dxpy) (0.4.4)
Requirement already satisfied: pyreadline3==3.4.1 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from dxpy) (3.4.1)
Requirement already satisfied: six in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from websocket-client==0.54.0->dxpy) (1.16.0)
Requirement already satisfied: cffi>=1.12 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from cryptography<37,>=3.4.2->dxpy) (1.15.1)
Requirement already satisfied: charset-normalizer~=2.0.0 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from requests<=2.27.1,>=2.8.0->dxpy) (2.0.12)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from requests<=2.27.1,>=2.8.0->dxpy) (1.26.11)
Requirement already satisfied: certifi>=2017.4.17 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from requests<=2.27.1,>=2.8.0->dxpy) (2022.6.15)
Requirement already satisfied: idna<4,>=2.5 in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from requests<=2.27.1,>=2.8.0->dxpy) (3.3)
Requirement already satisfied: pycparser in c:\users\fmc755\appdata\local\programs\python\python310\lib\site-packages (from cffi>=1.12->cryptography<37,>=3.4.2->dxpy) (2.21)
The folders seem to be added to following path "C:\Program Files (x86)\DNAnexus CLI\python27\Lib\site-packages" (see below) but when I use DNAnexus CLI, dx-toolkit still runs as v0.325.1.
I think this might be caused due to the path variable. You could try to follow this page and configure python3 as default.
https://superuser.com/questions/1399544/how-to-change-default-python-executable-on-windows-10
For avoiding such errors, I normally run dx-toolkit inside an isolated env (conda or virtualenv).
Thanks for your suggestions! I will give it a try.
I tried the solution with conda. Worked like a charm!
Thanks a lot.
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