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raphael-group / decifer

DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell fractions (DCF).
BSD 3-Clause "New" or "Revised" License
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generatestatetree usage #30

Closed Subhayan18 closed 4 months ago

Subhayan18 commented 4 months ago

Hello,

I am struggling using generatestatetree function. Could you please explain how to call it (unless compiling from decifer/build/lib/decifer/cpp/generatestatetreesmain.cpp) ?

gsatas commented 4 months ago

Hi Subhayan,

You can find brief instructions for using generatestatetrees in the "Addressing the "Skipping mutation warning" section" here. This should work directly from the conda build (I just tested it). Please let me know if you have any further questions or run into any errors.

Gryte

Subhayan18 commented 4 months ago

Hi Gryte,

Thank you for your fast response. So I suppose one can call the function in the activated conda environment? something akin to:

(/home/user/DeCiFer/decifer) @.*** ~]$ generatestatetrees CNA.tsv

Unfortunately I am getting missing prompt: bash: generatestatetrees: command not found...

Sorry, if I missing something very obvious.

Best, Subhayan

From: Gryte Satas @.***> Sent: Tuesday, May 21, 2024 3:49 PM To: raphael-group/decifer Cc: Subhayan; Author Subject: Re: [raphael-group/decifer] generatestatetree usage (Issue #30)

Hi Subhayan,

You can find brief instructions for using generatestatetrees in the "Addressing the "Skipping mutation warning" section" herehttps://github.com/raphael-group/decifer/tree/main/scripts#adressing-the-skipping-mutation-warning. This should work directly from the conda build (I just tested it). Please let me know if you have any further questions or run into any errors.

Gryte

— Reply to this email directly, view it on GitHubhttps://github.com/raphael-group/decifer/issues/30#issuecomment-2122684114, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AKMA52WH53D5EWE6IQLVAPTZDNGG3AVCNFSM6AAAAABIBRTIBWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRSGY4DIMJRGQ. You are receiving this because you authored the thread.Message ID: @.***>

gsatas commented 4 months ago

Can bash find decifer itself in your environment? That is, if you run which decifer, is the executable found?

Subhayan18 commented 4 months ago

Yes, it is in the environment and I can execute decifer with my own data

$which decifer ~/DeCiFer/decifer/bin/decifer

problem arises only when I want to invoke generatestatestree.

ps I followed the conda installation guide in the decifer manual.

Best, Subhayan

From: Gryte Satas @.***> Sent: Tuesday, May 21, 2024 4:11 PM To: raphael-group/decifer Cc: Subhayan; Author Subject: Re: [raphael-group/decifer] generatestatetree usage (Issue #30)

Can bash find decifer itself in your environment? That is, if you run which decifer, is the executable found?

— Reply to this email directly, view it on GitHubhttps://github.com/raphael-group/decifer/issues/30#issuecomment-2122730657, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AKMA52QCCXZW5WHIQSBGLMLZDNIXNAVCNFSM6AAAAABIBRTIBWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRSG4ZTANRVG4. You are receiving this because you authored the thread.Message ID: @.***>

gsatas commented 4 months ago

Did you follow the automatic or manual conda installation instructions? That is, did you run:

conda create -n decifer decifer -y -c bioconda
conda activate decifer

or did you run

git clone https://github.com/raphael-group/decifer.git && cd decifer/
conda create -c anaconda -c conda-forge -n decifer python=2.7 numpy scipy matplotlib-base pandas seaborn -y
pip install .

Based on the install location, I would guess the latter, in which case you'd have to also follow the "Installation of C++ component" instructions to run generatestatetrees. But the "automatic" installation instructions should include generatestatetrees without any further steps required.

Note: I did just add the "-c bioconda" flag to the automatic instructions, which should help in case you were running into a "decifer package not found" error when installing with the automatic instructions

Subhayan18 commented 4 months ago

Oh thanks!

Yes, I used a manual installation with updated Python version. I will give the automatic version a go too. Will keep you posted.

From: Gryte Satas @.***> Sent: Tuesday, May 21, 2024 4:55 PM To: raphael-group/decifer Cc: Subhayan; Author Subject: Re: [raphael-group/decifer] generatestatetree usage (Issue #30)

Did you follow the automatic or manual conda installation instructions? That is, did you run:

conda create -n decifer decifer -y -c bioconda conda activate decifer

or did you run

git clone https://github.com/raphael-group/decifer.git && cd decifer/ conda create -c anaconda -c conda-forge -n decifer python=2.7 numpy scipy matplotlib-base pandas seaborn -y pip install .

Based on the install location, I would guess the latter, in which case you'd have to also follow the "Installation of C++ component" instructions to run generatestatetrees. But the "automatic" installation instructions should include generatestatetrees without any further steps required.

Note: I did just add the "-c bioconda" flag to the automatic instructions, which should help in case you were running into a "decifer package not found" error when installing with the automatic instructions

— Reply to this email directly, view it on GitHubhttps://github.com/raphael-group/decifer/issues/30#issuecomment-2122825490, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AKMA52X7ZJQA7VAM3Z7CLRDZDNN47AVCNFSM6AAAAABIBRTIBWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRSHAZDKNBZGA. You are receiving this because you authored the thread.Message ID: @.***>