Unable to use python package

[christophgil]

Using Fragpipe 19.1

I psecified python
/opt/conda/envs/py39/bin/python

However it is not finding easypqp
I unset PYTHONPATH and still not finding easypqp

Checking installed easypqp
/opt/conda/envs/py39/bin/pip show easypqp
Name: easypqp
Version: 0.1.35
Summary: EasyPQP: Simple library generation for OpenSWATH
....
Location: /opt/conda/envs/py39/lib/python3.9/site-packages

Workaround:
Explicitely setting PYTHONPATH to /opt/conda/envs/py39/lib/python3.9/site-packages
solves this issue.

[fcyu]

I am sorry, but is there anything what we should fix or improve?

Thanks,

Fengchao

[christophgil]

with You have the path of the python binary. pip show easypqp you can detect the location of the local installation and then set PYTHONPATH in the script accordingly.

…

On Tue, Jan 24, 2023 at 7:09 PM Fengchao ***@***.***> wrote: I am sorry, but is there anything what we should fix or improve? Thanks, Fengchao — Reply to this email directly, view it on GitHub <#978 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASRZU6F5V3GPQHRX5QZ5M3TWUASFVANCNFSM6AAAAAAUFMHQFM> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[guoci]

@christophgil Can you enter in your terminal
/opt/conda/envs/py39/bin/python -m pip show --files easypqp
and show me the output?

[christophgil]

This is what is needed in my case: export PYTHONPATH=/opt/conda/envs/py39/lib/python3.9/site-packages /opt/conda/envs/py39/bin/python -m pip show --files easypqp Name: easypqp Version: 0.1.35 Summary: EasyPQP: Simple library generation for OpenSWATH Home-page: https://github.com/grosenberger/easypqp Author: George Rosenberger Author-email: ***@***.*** License: Location: /opt/conda/envs/py39/lib/python3.9/site-packages Requires: biopython, Click, matplotlib, numpy, pandas, pyopenms, scikit-learn, scipy, seaborn, statsmodels, tqdm Required-by: Files: ../../../bin/easypqp easypqp-0.1.35.dist-info/INSTALLER easypqp-0.1.35.dist-info/LICENSE easypqp-0.1.35.dist-info/METADATA easypqp-0.1.35.dist-info/RECORD easypqp-0.1.35.dist-info/REQUESTED easypqp-0.1.35.dist-info/WHEEL easypqp-0.1.35.dist-info/entry_points.txt easypqp-0.1.35.dist-info/top_level.txt easypqp/__init__.py easypqp/__pycache__/__init__.cpython-39.pyc easypqp/__pycache__/convert.cpython-39.pyc easypqp/__pycache__/library.cpython-39.pyc easypqp/__pycache__/main.cpython-39.pyc easypqp/__pycache__/test_convert.cpython-39.pyc easypqp/__pycache__/unimoddb.cpython-39.pyc easypqp/convert.py easypqp/data/unimod.xml easypqp/library.py easypqp/main.py easypqp/test_convert.py easypqp/unimoddb.py

…

On Wed, Jan 25, 2023 at 5:48 PM Guo Ci ***@***.***> wrote: @christophgil <https://github.com/christophgil> Can you enter in your terminal /opt/conda/envs/py39/bin/python -m pip show --files easypqp and show me the output? — Reply to this email directly, view it on GitHub <#978 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASRZU6G5FA2RF4KR5O35NXTWUFROTANCNFSM6AAAAAAUFMHQFM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[guoci]

@christophgil What happens if you unset PYTHONPATH? What is the output then?

[christophgil]

Works fine from command line. But in the Fragpipe GUI, easypqp is not recognized. I also tried export PYTHONPATH='' With the Runtime.exec java function, you can pass env variables. I suggest that you first run the pip show command from java to determine the location and then run python with Runtime.exec with the env variable specified. Here the output: unset PYTHONPATH # No matter whether unset or export to any nonsense string. Always works /opt/conda/envs/py39/bin/python -m pip show --files easypqp Name: easypqp Version: 0.1.35 Summary: EasyPQP: Simple library generation for OpenSWATH Home-page: https://github.com/grosenberger/easypqp Author: George Rosenberger Author-email: ***@***.*** License: Location: /opt/conda/envs/py39/lib/python3.9/site-packages Requires: biopython, Click, matplotlib, numpy, pandas, pyopenms, scikit-learn, scipy, seaborn, statsmodels, tqdm Required-by: Files: ../../../bin/easypqp

…

On Thu, Jan 26, 2023 at 5:19 PM Guo Ci ***@***.***> wrote: @christophgil <https://github.com/christophgil> What happens if you unset PYTHONPATH? What is the output then? — Reply to this email directly, view it on GitHub <#978 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASRZU6FDRRQ4B3JRC472EXLWUKPYHANCNFSM6AAAAAAUFMHQFM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[guoci]

@christophgil you are using a conda env and the commands you run needs conda activate.
The problem is when you run FragPipe you did not do conda activate before starting it.

[christophgil]

Thanks! Another issue I had was to use a global FragPipe installation for different users such that each user can have its own settings and configuration. I was expecting that the local config files maybe in ~/.fragpipe/ take precedence over the global fragpipe-runtime.cache and fragpipe-ui.cache Is this supposed to work or should each user have it's own installation? I solved this by embeding the global installation in an overlay FS (unionfs-fuse) so it works for us. Best Christoph

…

On Mon, Jan 30, 2023 at 6:19 PM Guo Ci ***@***.***> wrote: @christophgil <https://github.com/christophgil> you are using a conda env and the commands you run needs conda activate. The problem is when you run FragPipe you did not do conda activate before starting it. — Reply to this email directly, view it on GitHub <#978 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASRZU6BMY7NT5XYZCBIOL3LWVAA3FANCNFSM6AAAAAAUFMHQFM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[fcyu]

Hi Christoph,

Can you try if configuring the temp file directory works for you: #755 (comment) ?

Also, FragPipe's config directory is in HOME. There should be no issue for multi-user scenario.

Thanks,

Fengchao

[christophgil]

Hi Fengchao, Please let me ask a question on file names. we observed that Fragpipe does not work on bruker file folders that have a dot in the name. Therefore we need to rename files like 20230102_abcd_0.5ug_defg.d into 20230102_abcd_0_5ug_defg.d. Could dots in the name be supported? Best Christoph

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On Tue, Jan 31, 2023 at 5:52 PM Fengchao ***@***.***> wrote: Hi Christoph, Can you try if configuring the temp file directory works for you: #755 (comment) <#755 (comment)> ? Thanks, Fengchao — Reply to this email directly, view it on GitHub <#978 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASRZU6HGCXH7BIMV7WR5KKTWVFGOZANCNFSM6AAAAAAUFMHQFM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[fcyu]

Hi Christoph,

Some tools, such as PeptideProphet if I remember it correctly, have some issues when there is a dot in the file name. That is why FragPipe wants you to rename the file.

But, you can skip the renaming step by clicking "try to rename files" and then "no":

Best,

Fengchao

[christophgil]

Thank you! Our files are already in a WORM storage. I will try to make a virtual file system were the files are presented with a fake name. Best Christoph

…

On Sun, Feb 5, 2023 at 10:26 PM Fengchao ***@***.***> wrote: Hi Christoph, Some tools, such as PeptideProphet if I remember it correctly, have some issues when there is a dot in the file name. That is why FragPipe wants you to rename the file. But, you can skip the renaming step by clicking "try to rename files" and then "no": [image: image] <https://user-images.githubusercontent.com/6926299/216849409-816f372f-1ae8-43e3-9827-c79ac9e566db.png> [image: image] <https://user-images.githubusercontent.com/6926299/216849422-7e575dc7-8e2f-497b-88b3-fd4fce1e0a9c.png> Best, Fengchao — Reply to this email directly, view it on GitHub <#978 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASRZU6AUXWK6V3H53P4FT53WWASJRANCNFSM6AAAAAAUFMHQFM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[christophgil]

Hi Fengchao, I am working on a virtual FS and notice that extremely often access to these non existing files are requested which creates a performance problem: analysis.tdf-journal analysis.tdf-wal I guess the Bruker code is responsible is'nt it? Is this open source code so I could inspect the code? Best Christoph

…

On Mon, Feb 6, 2023 at 1:24 PM Fengchao ***@***.***> wrote: Closed #978 <#978> as completed. — Reply to this email directly, view it on GitHub <#978 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASRZU6C6VMY4CGCWMRHP3ZDWWD3QJANCNFSM6AAAAAAUFMHQFM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[fcyu]

Hi Christoph,

I guess the Bruker code is responsible is'nt it?

Yes.

Is this open source code so I could inspect the code?

No.

BTW, you actually no need to work on the virtual FS because you don't have to rename the file name. See my last comment: #978 (comment)

Best,

Fengchao

[christophgil]

Cool! Nevertheless, we have zip files in a WORM Currently we mount, the zips,but this is awkward. Best Christoph

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On Wed, Feb 8, 2023 at 10:30 PM Fengchao ***@***.***> wrote: Hi Christoph, I guess the Bruker code is responsible is'nt it? Yes. Is this open source code so I could inspect the code? No. BTW, you actually no need to work on the virtual FS because you don't have to rename the file name. See my last comment: #978 (comment) <#978 (comment)> Best, Fengchao — Reply to this email directly, view it on GitHub <#978 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASRZU6CAWFSUGJRF7IHNELTWWQNBBANCNFSM6AAAAAAUFMHQFM> . You are receiving this because you were mentioned.Message ID: ***@***.***>