Deblur installation error

[EmmettPeng]

Hi,

I have followed installation manuscript to use conda to install Deblur. After running:

conda create -n deblurenv python=3.5 numpy
source activate deblurenv
conda install -c bioconda -c biocore "VSEARCH=2.7.0" MAFFT=7.310 SortMeRNA=2.0 biom-format deblur

I ran the command deblur workflow --help but error occured:

(deblurenv) galaxy@r920:~/galaxytest/galaxy$ deblur workflow --help
Traceback (most recent call last):
  File "/softwares/miniconda3/envs/deblurenv/bin/deblur", line 11, in <module>
    import click
  File "/softwares/miniconda3/envs/deblurenv/lib/python3.5/site-packages/click/__init__.py", line 7, in <module>
    from .core import Argument
  File "/softwares/miniconda3/envs/deblurenv/lib/python3.5/site-packages/click/core.py", line 99
    f"{hint}. Command {base_command.name!r} is set to chain and"
                                                               ^
SyntaxError: invalid syntax

I am not sure where it went south. Any help would be greatly appreciated!

Regards Emmett

[mortonjt]

hmm that is weird. Can you provide the version of click? This error is hinting at some conflict between click and maybe pythonn=3.5

On Mon, May 24, 2021 at 8:05 AM Emmett Peng @.***> wrote:

Hi,

I have followed installation manuscript to use conda to install Deblur. After running:

conda create -n deblurenv python=3.5 numpy source activate deblurenv conda install -c bioconda -c biocore "VSEARCH=2.7.0" MAFFT=7.310 SortMeRNA=2.0 biom-format deblur

I ran the command deblur workflow --help but error occured:

(deblurenv) @.***:~/galaxytest/galaxy$ deblur workflow --help Traceback (most recent call last): File "/softwares/miniconda3/envs/deblurenv/bin/deblur", line 11, in import click File "/softwares/miniconda3/envs/deblurenv/lib/python3.5/site-packages/click/init.py", line 7, in from .core import Argument File "/softwares/miniconda3/envs/deblurenv/lib/python3.5/site-packages/click/core.py", line 99 f"{hint}. Command {base_command.name!r} is set to chain and" ^ SyntaxError: invalid syntax

I am not sure where it went south. Any help would be greatly appreciated!

Regards Emmett

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[EmmettPeng]

hmm that is weird. Can you provide the version of click? This error is hinting at some conflict between click and maybe pythonn=3.5 … On Mon, May 24, 2021 at 8:05 AM Emmett Peng @.> wrote: Hi, I have followed installation manuscript to use conda to install Deblur. After running: conda create -n deblurenv python=3.5 numpy source activate deblurenv conda install -c bioconda -c biocore "VSEARCH=2.7.0" MAFFT=7.310 SortMeRNA=2.0 biom-format deblur I ran the command deblur workflow --help but error occured: (deblurenv) @.:~/galaxytest/galaxy$ deblur workflow --help Traceback (most recent call last): File "/softwares/miniconda3/envs/deblurenv/bin/deblur", line 11, in import click File "/softwares/miniconda3/envs/deblurenv/lib/python3.5/site-packages/click/init.py", line 7, in from .core import Argument File "/softwares/miniconda3/envs/deblurenv/lib/python3.5/site-packages/click/core.py", line 99 f"{hint}. Command {base_command.name!r} is set to chain and" ^ SyntaxError: invalid syntax I am not sure where it went south. Any help would be greatly appreciated! Regards Emmett — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#207>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA75VXNUFYA3PC6ZCJBF7BTTPJMK3ANCNFSM45NJP4MQ .

Click is of version 8.0.0

(deblurenv) galaxy@r920:/softwares$ pip show click
Name: click
Version: 8.0.0
Summary: Composable command line interface toolkit
Home-page: https://palletsprojects.com/p/click/
Author: Armin Ronacher
Author-email: armin.ronacher@active-4.com
License: BSD-3-Clause
Location: /softwares/miniconda3/envs/deblurenv/lib/python3.5/site-packages
Requires: 
Required-by: deblur, biom-format

[mortonjt]

Got it. See here : https://click.palletsprojects.com/en/8.0.x/changes/#version-8-0-0

Python3.5 compatibility is no longer supported with click. So I'd try to either downgrade click to 7.1.1 or upgrade python=3.6

On Mon, May 24, 2021 at 8:20 AM Emmett Peng @.***> wrote:

hmm that is weird. Can you provide the version of click? This error is hinting at some conflict between click and maybe pythonn=3.5 … <#m-7279960139194607740> On Mon, May 24, 2021 at 8:05 AM Emmett Peng @.> wrote: Hi, I have followed installation manuscript to use conda to install Deblur. After running: conda create -n deblurenv python=3.5 numpy source activate deblurenv conda install -c bioconda -c biocore "VSEARCH=2.7.0" MAFFT=7.310 SortMeRNA=2.0 biom-format deblur I ran the command deblur workflow --help but error occured: (deblurenv) @.:~/galaxytest/galaxy$ deblur workflow --help Traceback (most recent call last): File "/softwares/miniconda3/envs/deblurenv/bin/deblur", line 11, in import click File "/softwares/miniconda3/envs/deblurenv/lib/python3.5/site-packages/click/ init.py", line 7, in from .core import Argument File "/softwares/miniconda3/envs/deblurenv/lib/python3.5/site-packages/click/core.py", line 99 f"{hint}. Command {base_command.name!r} is set to chain and" ^ SyntaxError: invalid syntax I am not sure where it went south. Any help would be greatly appreciated! Regards Emmett — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#207 https://github.com/biocore/deblur/issues/207>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA75VXNUFYA3PC6ZCJBF7BTTPJMK3ANCNFSM45NJP4MQ .

Click is of version 8.0.0

(deblurenv) @.***:/softwares$ pip show click

Name: click

Version: 8.0.0

Summary: Composable command line interface toolkit

Home-page: https://palletsprojects.com/p/click/

Author: Armin Ronacher

Author-email: @.***

License: BSD-3-Clause

Location: /softwares/miniconda3/envs/deblurenv/lib/python3.5/site-packages

Requires:

Required-by: deblur, biom-format

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/biocore/deblur/issues/207#issuecomment-847075414, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA75VXO2ZQHTHFOKVRFU7YDTPJOB3ANCNFSM45NJP4MQ .

[EmmettPeng]

Got it. See here : https://click.palletsprojects.com/en/8.0.x/changes/#version-8-0-0 Python3.5 compatibility is no longer supported with click. So I'd try to either downgrade click to 7.1.1 or upgrade python=3.6 On Mon, May 24, 2021 at 8:20 AM Emmett Peng @.> wrote: … hmm that is weird. Can you provide the version of click? This error is hinting at some conflict between click and maybe pythonn=3.5 … <#m-7279960139194607740> On Mon, May 24, 2021 at 8:05 AM Emmett Peng @.> wrote: Hi, I have followed installation manuscript to use conda to install Deblur. After running: conda create -n deblurenv python=3.5 numpy source activate deblurenv conda install -c bioconda -c biocore "VSEARCH=2.7.0" MAFFT=7.310 SortMeRNA=2.0 biom-format deblur I ran the command deblur workflow --help but error occured: (deblurenv) @.:~/galaxytest/galaxy$ deblur workflow --help Traceback (most recent call last): File "/softwares/miniconda3/envs/deblurenv/bin/deblur", line 11, in import click File "/softwares/miniconda3/envs/deblurenv/lib/python3.5/site-packages/click/ init.py", line 7, in from .core import Argument File "/softwares/miniconda3/envs/deblurenv/lib/python3.5/site-packages/click/core.py", line 99 f"{hint}. Command {base_command.name!r} is set to chain and" ^ SyntaxError: invalid syntax I am not sure where it went south. Any help would be greatly appreciated! Regards Emmett — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#207 <#207>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA75VXNUFYA3PC6ZCJBF7BTTPJMK3ANCNFSM45NJP4MQ . Click is of version 8.0.0 (deblurenv) @.:/softwares$ pip show click Name: click Version: 8.0.0 Summary: Composable command line interface toolkit Home-page: https://palletsprojects.com/p/click/ Author: Armin Ronacher Author-email: @.*** License: BSD-3-Clause Location: /softwares/miniconda3/envs/deblurenv/lib/python3.5/site-packages Requires: Required-by: deblur, biom-format — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#207 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA75VXO2ZQHTHFOKVRFU7YDTPJOB3ANCNFSM45NJP4MQ .

Thanks for your reply! The problem went away after upgrading python=3.6.

[mortonjt]

Great!! Closing this issue. Feel free to follow up if there are outstanding problems.