bioconda recipe

[Takadonet]

Request to have a bioconda recipe created for ease of installation.

https://bioconda.github.io/index.html

[mw55309]

+1

This would really aid installation!

[elzerac]

Yes please! Another vote for this.

[donovan-h-parks]

We have no immediate plans to create a Bioconda recipe, but would certainly be grateful if someone wanted to create such a recipe.

[npavlovikj]

@dparks1134 , I needed a bioconda recipe for "gtdbtk", so I created one, https://anaconda.org/bioconda/gtdbtk. The download of the database is not part of the recipe, but there is a "download-db.sh" script that does that when ran from the conda environment. You can see the full recipe here, https://github.com/bioconda/bioconda-recipes/tree/3be50c3157c5324d60030bfa74f6b2e1b7f7e159/recipes/gtdbtk.

I hope you and the "gtdbtk" users find the conda package useful. I have had only 2 people use the environment so far, but if there are any issues with the recipe, I would be more than happy to fix and update things.

[donovan-h-parks]

Thanks Natasha! I have added this to the GTDB-Tk readme file.

[chloelulu]

Hi, @npavlovikj ,

Thanks for creating the bioconda recipe. May I know is it still currently available? Since I tried both 'conda install -c bioconda gtdbtk' and 'conda install -c bioconda/label/cf201901 gtdbtk'. It is always under Collecting package metadata: done Solving environment: More than 24 hours, it is still under this status Any possible way to solve it? Thanks.

[npavlovikj]

Hey @chloelulu ! Yes, the bioconda "gtdbtk" package is still available. I just tried installing it myself with conda create -n gtdbtk gtdbtk, and that worked fine.

Using conda create is recommended over conda install, so can you please try that instead? Sometimes, the current environment may have dependencies that are not compatible with the new package you want to install, so creating a new environment is always better. Also, not having the proper channel order may cause the install to be stuck at the "Solving environment" stage. If conda create doesn't work, can you make sure you add the following channel order conda create -n gtdbtk -c conda-forge -c bioconda -c defaults gtdbtk?

I hope these suggestions help, and please let me know if any works for you.

[chloelulu]

Hi, @npavlovikj , Amazing. It works well with conda create -n gtdbtk gtdbtk. Thanks so much! It is much much much better to use conda install!!! Appreciate your help!

[chloelulu]

Hi, @npavlovikj ,

May I please follow up another question. Since I use conda create -n gtdbtk gtdbtk and the version of gtdbtk is version 0.1.5 Copyright 2017 Pierre Chaumeil. But there is a bug in the current version. I got the same error as described here https://github.com/Ecogenomics/GTDBTk/issues/83 So I need to update the current version to 0.1.6. May I know how to achieve that? Thanks so much!

[npavlovikj]

@chloelulu , for every new release of GTDBTk, the bioconda recipe itself needs to be updated. I went ahead and did this, and now gtdbtk 0.1.6 is available on bioconda. If you repeat the steps from above (or you can use conda create -n gtdbtk gtdbtk=0.1.6), the newest version will be installed. I haven't fully tested this version, so if you encounter any issues with the bioconda package, please let me know.

[chloelulu]

Hi, @npavlovikj It is amazing for you to have compiled a new version so quickly. I have tested it just now. The installation has no problem. But error occurs here Uncaught exception: Failure("Sequence bin.359.filtered.filtered.filtered doesn't overlap any reference sequences.") Fatal error: exception Failure("Sequence bin.359.filtered.filtered.filtered doesn't overlap any reference sequences.") Uncaught exception: Sys_error("gtdbtk/pplacer/pplacer.bac120.json: No such file or directory") Fatal error: exception Sys_error("gtdbtk/pplacer/pplacer.bac120.json: No such file or directory") GTDB-Tk has stopped before finishing [Errno 2] No such file or directory: 'gtdbtk/gtdbtk.bac120.classify.tree' ('Unexpected error:', <type 'exceptions.IOError'>) But I manually installed by pip. I have successfully run.

[npavlovikj]

@chloelulu - I did a small test with both the conda and pip installs, and I got the same error as you did in both cases. Therefore, I don't think the issue is with the conda recipe. It looks like other people have observed the same error (https://github.com/Ecogenomics/GTDBTk/issues/78, https://github.com/Ecogenomics/GTDBTk/issues/70). The error happens at the pplacer step, highly likely because pplacer exceeds the available memory. Did you maybe use the pip install with higher memory, and thus that installation worked for you?

[chloelulu]

Hi, @npavlovikj , You are so patient. This error does not happen to me when I use the pip install. And my install always on the same server, I am not sure whether it includes a higher memory.

[cssulliv]

Hi, I am new to to gtdbtk and am a novice python coder so I hope you can help me with this :) I have attempted to install gtdbtk using the scripts listed below and I have gotten the same error message: Collecting package metadata: done

Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

• gtdbtk -> pplacer

Current channels:

• https://conda.anaconda.org/conda-forge/osx-64
• https://conda.anaconda.org/conda-forge/noarch
• https://conda.anaconda.org/bioconda/osx-64
• https://conda.anaconda.org/bioconda/noarch
• https://repo.anaconda.com/pkgs/main/osx-64
• https://repo.anaconda.com/pkgs/main/noarch
• https://repo.anaconda.com/pkgs/free/osx-64
• https://repo.anaconda.com/pkgs/free/noarch
• https://repo.anaconda.com/pkgs/r/osx-64
• https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

Scripts I had used:

conda create -n gtdbtk -c conda-forge -c bioconda -c defaults gtdbtk

conda create -n gtdbtk gtdbtk

conda create -n gtdbtk -c bioconda gtdbtk

conda create -n gtdbtk -c bioconda/label/cf201901 gtdbtk

I was wondering what mistake I was making and how to fix it so I can download gtdbtk.

[aaronmussig]

Hello, are you running on OSX by any chance? So far bioconda only has supports pplacer on Linux Linux (although it can be unofficially run on OSX).

Apologies if that's the case. The bioconda recipe states it's platform-independent as I couldn't figure out how to get it to pass linting as linux-only. If it's the case, try creating a python 2.7 conda environment and pip installing it in there instead.

[cssulliv]

Hi,

I am indeed using OSX. I will give it a try with pip. Thank you for letting me know!

I'll reach out again if I have further questions :)

Best, Clarisse

On Tue, Jul 23, 2019 at 5:47 PM Aaron notifications@github.com wrote:

Hello, are you running on OSX by any chance? So far bioconda only has supports pplacer on Linux Linux (although it can be unofficially run on OSX).

Apologies if that's the case. The bioconda recipe states it's platform-independent as I couldn't figure out how to get it to pass linting as linux-only. If it's the case, try creating a python 2.7 conda environment and pip installing it in there instead.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Ecogenomics/GTDBTk/issues/30?email_source=notifications&email_token=AJ3Z5B554H4NUCPALE4WZLLQA7GEPA5CNFSM4FR7A3J2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2VCQUY#issuecomment-514467923, or mute the thread https://github.com/notifications/unsubscribe-auth/AJ3Z5B47WXY7EUUVS76AATLQA7GEPANCNFSM4FR7A3JQ .

--

Clarisse Eleanor S. Sullivan https://cssulliv716.wixsite.com/website Graduate Student, Biological Oceanography M.S. Program The Rappe Lab https://rappelab.wordpress.com/

Lab Phone No.: 808-236-7465 Cell No.: 401-263-6163

Hawai'i Institute of Marine Biology PO BOX 1346 (for US Postal Service) 46-007 Lilipuna Road (for deliveries) University of Hawaii at Manoa Kaneohe, HI 96744