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LooseLab / readfish

CLI tool for flexible and fast adaptive sampling on ONT sequencers
https://looselab.github.io/readfish/
GNU General Public License v3.0
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Installing ReadFish on GridION #200

Closed melkramer closed 2 years ago

melkramer commented 2 years ago

Hello,

Could you please advise on the current method to install readfish? I'm trying to install readfish for Guppy V6 as in Issue #170 but am getting this error:

python3 -m venv readfish

. readfish/bin/activate

(readfish) # pip3 install --upgrade pip Collecting pip Using cached https://files.pythonhosted.org/packages/96/2f/caec18213f6a67852f6997fb0673ae08d2e93d1b81573edb93ba4ef06970/pip-22.1.2-py3-none-any.whl Installing collected packages: pip Found existing installation: pip 8.1.1 Uninstalling pip-8.1.1: Successfully uninstalled pip-8.1.1 Successfully installed pip-22.1.2 (readfish) # pip install git+https://github.com/nanoporetech/read_until_api@v3.0.0 Traceback (most recent call last): File "/root/readfish/bin/pip", line 7, in from pip._internal.cli.main import main File "/root/readfish/lib/python3.5/site-packages/pip/_internal/cli/main.py", line 57 sys.stderr.write(f"ERROR: {exc}") ^ SyntaxError: invalid syntax

Thank you, Melissa

alexomics commented 2 years ago

Hi Melissa,

It looks like your python3 executable is using Python v3.5 and that the upgraded version of pip is not compatible with python 3.5.

For readfish we require a newer python version, ≥3.7. There are some instructions for using conda to setup readfish in issue #124.

Let me know if you are able to install readfish using the linked instructions.

Alex

melkramer commented 2 years ago

Thank you, after updating to python 3.8 the conda setup is working!

Best,

Melissa

From: alex @.***> Sent: Wednesday, June 8, 2022 10:50:02 AM To: LooseLab/readfish Cc: delaBastide, Melissa; Author Subject: Re: [LooseLab/readfish] Installing ReadFish on GridION (Issue #200)

Hi Melissa,

It looks like your python3 executable is using Python v3.5 and that the upgraded version of pip is not compatible with python 3.5.

For readfish we require a newer python version, ≥3.7. There are some instructions for using conda to setup readfish in issue #124https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_LooseLab_readfish_issues_124-23issuecomment-2D759599319&d=DwMFaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=YkQFpFMc1TX4EpPMAcLbOFRrB-GWTkBhuseQ_TTscv4&m=6JqnjG4Z6X6N5_Q9g-K7QAdpWtafxiLHYNwKd6PfPIz3xfESIFc16EPgDAX_HwVd&s=7vdd3Wbqo5zY1_puiAZhpSN826xqoz8g8aoFNa1kP4o&e=.

Let me know if you are able to install readfish using the linked instructions.

Alex

― Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_LooseLab_readfish_issues_200-23issuecomment-2D1150023500&d=DwMFaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=YkQFpFMc1TX4EpPMAcLbOFRrB-GWTkBhuseQ_TTscv4&m=6JqnjG4Z6X6N5_Q9g-K7QAdpWtafxiLHYNwKd6PfPIz3xfESIFc16EPgDAX_HwVd&s=c-dKMSikOhPcBcvsKjgAdRKTm7wrMdkuMHi_0VHNWQ4&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ATP2RAO4P6I4D2EVE4VJL63VOCXJVANCNFSM5YGZB77Q&d=DwMFaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=YkQFpFMc1TX4EpPMAcLbOFRrB-GWTkBhuseQ_TTscv4&m=6JqnjG4Z6X6N5_Q9g-K7QAdpWtafxiLHYNwKd6PfPIz3xfESIFc16EPgDAX_HwVd&s=5a2bTd8MPNVoVzmO1feyK90p13kuhtdwwAY7O-B9ynI&e=. You are receiving this because you authored the thread.Message ID: @.***>

alexomics commented 2 years ago

Fantastic! If you run into any other problems, please open a new issue.