Install MAESTRO version 1.2.1.9999

[ryao-mdanderson]

I followed the instruction https://github.com/liulab-dfci/MAESTRO to install MAESTRO on HPC cluster for our institution research community.

My python version is 3.7.3-anaconda; conda version 4.9.2-py37h89c1867_0

I followed the instruction “ Installing the full solution of MAESTRO workflow through conda “, here is my procedures

[ris_hpc_apps@tdragon4 ~]$ module load python/3.7.3-anaconda

[ris_hpc_apps@tdragon4 ~]$ which conda

/risapps/rhel7/python/3.7.3/bin/conda

[ris_hpc_apps@tdragon4 ~]$ conda config --add channels defaults

Warning: 'defaults' already in 'channels' list, moving to the top

[ris_hpc_apps@tdragon4 ~]$ conda config --add channels bioconda

Warning: 'bioconda' already in 'channels' list, moving to the top

[ris_hpc_apps@tdragon4 ~]$ conda config --add channels conda-forge

Warning: 'conda-forge' already in 'channels' list, moving to the top

   -- no need to add those channels; they are already there.

[ris_hpc_apps@tdragon4 ~]$ conda install mamba -c conda-forge

Collecting package metadata (repodata.json): done

Solving environment: done

## Package Plan ##

  environment location: /risapps/rhel7/python/3.7.3

  added / updated specs:

    - mamba

The following packages will be downloaded:

    package                    |            build

    ---------------------------|-----------------

    ca-certificates-2020.11.8  |       ha878542_0         145 KB  conda-forge

    certifi-2020.11.8          |   py37h89c1867_0         150 KB  conda-forge

    conda-4.9.2                |   py37h89c1867_0         3.0 MB  conda-forge

    libsolv-0.7.16             |       h8b12597_0         455 KB  conda-forge

    ------------------------------------------------------------

                                           Total:         3.8 MB

The following NEW packages will be INSTALLED:

  libsolv            conda-forge/linux-64::libsolv-0.7.16-h8b12597_0

  mamba              conda-forge/linux-64::mamba-0.1.2-py37h99015e2_0

The following packages will be UPDATED:

  ca-certificates                      2020.6.20-hecda079_0 --> 2020.11.8-ha878542_0

  certifi                          2020.6.20-py37he5f6b98_2 --> 2020.11.8-py37h89c1867_0

  conda                                4.9.0-py37he5f6b98_1 --> 4.9.2-py37h89c1867_0

Proceed ([y]/n)? *y*

# I choose yes to update the conda to the latest version here

 Downloading and Extracting Packages

libsolv-0.7.16       | 455 KB    | ########################################################### | 100%

 certifi-2020.11.8    | 150 KB    | ########################################################### | 100%

 ca-certificates-2020 | 145 KB    | ########################################################### | 100%

 conda-4.9.2          | 3.0 MB    | ########################################################### | 100%

 Preparing transaction: done

Verifying transaction: done

Executing transaction: done

[ris_hpc_apps@tdragon4 ~]$ mamba create -n MAESTRO-1.2.1 -c liulab-dfci

  (since we already have MAESTO created for version 1.0.1, I choose a different conda environment name MAESTRO-1.2.1  )

  .......

   Getting  liulab-dfci linux-64

Getting  liulab-dfci noarch

Getting  conda-forge linux-64

Getting  conda-forge noarch

Getting  bioconda linux-64

Getting  bioconda noarch

Getting  pkgs/main linux-64

Getting  pkgs/main noarch

Getting  pkgs/r noarch

Getting  r linux-64

Getting  pkgs/r linux-64

Getting  dranew linux-64

Getting  r noarch

Getting  dranew noarch

Looking for: []

9 packages in https://conda.anaconda.org/liulab-dfci/linux-64

0 packages in https://conda.anaconda.org/liulab-dfci/noarch

139892 packages in https://conda.anaconda.org/conda-forge/linux-64

43184 packages in https://conda.anaconda.org/conda-forge/noarch

33562 packages in https://conda.anaconda.org/bioconda/linux-64

21237 packages in https://conda.anaconda.org/bioconda/noarch

18648 packages in https://repo.anaconda.com/pkgs/main/linux-64

2356 packages in https://repo.anaconda.com/pkgs/main/noarch

6637 packages in https://repo.anaconda.com/pkgs/r/linux-64

5025 packages in https://repo.anaconda.com/pkgs/r/noarch

6620 packages in https://conda.anaconda.org/r/linux-64

5025 packages in https://conda.anaconda.org/r/noarch

170 packages in https://conda.anaconda.org/dranew/linux-64

0 packages in https://conda.anaconda.org/dranew/noarch

## Package Plan ##

  environment location: /risapps/rhel7/python/3.7.3/envs/MAESTRO-1.2.1

Proceed ([y]/n)? y

 #
  # To activate this environment, use
  #
  #     $ conda activate MAESTRO-1.2.1
  #
  # To deactivate an active environment, use
  #
  #     $ conda deactivate

Preparing transaction: done

Verifying transaction: done

Executing transaction: done

At this point, I check the environment directory /risapps/rhel7/python/3.7.3/envs/MAESTRO-1.2.1;

I only notice one directory was generated, is this normal?

[ris_hpc_apps@tdragon4 MAESTRO]$ ls -l /risapps/rhel7/python/3.7.3/envs/MAESTRO-1.2.1

total 0

drwxr-xr-x 2 ris_hpc_apps rists 29 Nov 20 16:07 conda-meta

Note: I used our software installation account ris_hpc_apps to install this on HPC cluster. I suppose to let user to do "conda activate MAESTRO-1.2.1" ( "conda init bash" is needed before this)

Regards, Rong

[taoliu]

After you created the environment by 'mamba create -n MAESTRO-1.2.1 -c liulab-dfci', you didn't install anything in that environment... You should either create the environment by:

mamba create -n MAESTRO-1.2.1 maestro=1.2.1.9999 -c liulab-dfci

or activate the environment then install:

conda activate MAESTRO-1.2.1 mamba install maestro=1.2.1.9999

Please note that 1.2.1.9999 is a beta version for 1.2.2 so it may not be able to successfully run. Please use version 1.2.1 at this stage, and we will release the stable version 1.2.2 soon. We just need more internal testing.

-T

[ryao-mdanderson]

Hello Tao,

Thanks for the tips.

If I do want to install version 1.2.1 (instead of test version 1.2.1.9999), should I use the command after 'mamba create -n MAESTRO-1.2.1 -c liulab-dfci' ?

mamba create -n MAESTRO-1.2.1 maestro=1.2.1 -c liulab-dfci Thanks! Rong

From: "Tao Liu (τν)" notifications@github.com Reply-To: liulab-dfci/MAESTRO reply@reply.github.com Date: Monday, November 23, 2020 at 9:03 AM To: liulab-dfci/MAESTRO MAESTRO@noreply.github.com Cc: "Yao,Rong" RYao@mdanderson.org, Author author@noreply.github.com Subject: [EXT] Re: [liulab-dfci/MAESTRO] Install MAESTRO version 1.2.1.9999 (#80)

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After you created the environment by 'mamba create -n MAESTRO-1.2.1 -c liulab-dfci', you didn't install anything in that environment... You should either create the environment by:

mamba create -n MAESTRO-1.2.1 maestro=1.2.1.9999 -c liulab-dfci

or activate the environment then install:

conda activate MAESTRO-1.2.1 mamba install maestro=1.2.1.9999

Please note that 1.2.1.9999 is a beta version for 1.2.2 so it may not be able to successfully run. Please use version 1.2.1 at this stage, and we will release the stable version 1.2.2 soon. We just need more internal testing.

-T

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[taoliu]

If you have already created the environment, then do this:

conda activate MAESTRO-1.2.1
mamba install maestro=1.2.1

[ryao-mdanderson]

Hello Tao,

conda activate MAESTRO-1.2.1 requires to initialize shell environment first, e.g. conda init bash;

I use a service account ris_hpc_apps to do installation on HPC, I do not wish to do conda init bash for the service account.

Is there any other options? For earlier version, we can do:

“conda create -n MAESTRO maestro -c liulab-dfci”

I am not sure if “conda create -n MAESTRO-1.2.1 maestro=1.2.1 -c liulab-dfci” achieves same effect?

If yes, we can ask user to do conda activate MAESTRO-1.2.1 at use level.

Thanks,

Rong

From: "Tao Liu (τν)" notifications@github.com Reply-To: liulab-dfci/MAESTRO reply@reply.github.com Date: Monday, November 23, 2020 at 11:02 AM To: liulab-dfci/MAESTRO MAESTRO@noreply.github.com Cc: "Yao,Rong" RYao@mdanderson.org, Author author@noreply.github.com Subject: [EXT] Re: [liulab-dfci/MAESTRO] Install MAESTRO version 1.2.1.9999 (#80)

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If you have already created the environment, then do this:

conda activate MAESTRO-1.2.1

mamba install maestro=1.2.1

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[crazyhottommy]

Hi @ryao-mdanderson do you still have problems installing? I recommend trying the newest v1.2.2 version.

[ryao-mdanderson]

Hello Ming,

Thank you! I will install the newest version 1.2.2.

Regards, Rong

From: Ming Tang notifications@github.com Reply-To: liulab-dfci/MAESTRO reply@reply.github.com Date: Friday, December 11, 2020 at 9:15 AM To: liulab-dfci/MAESTRO MAESTRO@noreply.github.com Cc: "Yao,Rong" RYao@mdanderson.org, Mention mention@noreply.github.com Subject: [EXT] Re: [liulab-dfci/MAESTRO] Install MAESTRO version 1.2.1.9999 (#80)

WARNING: This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe.

Hi @ryao-mdandersonhttps://urldefense.com/v3/__https:/github.com/ryao-mdanderson__;!!PfbeBCCAmug!35zLZp3anqy3LgVwkf1hash5AbbmzN1yHz5p-pfrOJ2H-p-Cx6w8z8Tkumbd8Cg$ do you still have problems installing? I recommend trying the newest v1.2.2 version.

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[ryao-mdanderson]

I am able to install MAESTRO 1.2.2 with module load R/4.0.0, no errors. Is R/4.0.0 sufficient? documentation requires R (>= 4.0.2).

[crazyhottommy]

great! R is installed inside the MAESTRO conda env, so no need to do module load.

[ryao-mdanderson]

Thank you! 💯

[ryao-mdanderson]

You might close this ticket. Thanks for all your helps.

[crazyhottommy]

No problem. feel free to open new issues if you have questions.