search

QFAB-Bioinformatics / metaDEGalaxy

GNU General Public License v3.0
0 stars 1 forks source link

Move phyloseq to IUC #2

Open bernt-matthias opened 1 year ago

bernt-matthias commented 1 year ago

Thanks for contributing these phyloseq tools.

I'm wondering if we could integrate these tools into the IUC repository: https://github.com/galaxyproject/tools-iuc/blob/master/tools/phyloseq/?

mthang commented 1 year ago

Hi Matthais, We do not see any issues to integrate the phyloseq tools into the IUC repository. Please let us know if you have any questions.

Many thanks, Mike

Mike Thang Bioinformatician, QCIF Facility for Advanced Bioinformatics

Queensland Cyber Infrastructure Foundation (QCIF)

BIOINFORMATICS | BIOSTATISTICS | BIODATA | BIO IT

[cid:8f4d43da-9ce3-4feb-9d7b-b10605b9a00b]

From: M Bernt @.> Sent: Thursday, 6 October 2022 6:48 PM To: QFAB-Bioinformatics/metaDEGalaxy @.> Cc: Subscribed @.***> Subject: [QFAB-Bioinformatics/metaDEGalaxy] Move phyloseq to IUC (Issue #2)

Thanks for contributing these phyloseq tools.

I'm wondering if we could integrate these tools into the IUC repository: https://github.com/galaxyproject/tools-iuc/blob/master/tools/phyloseq/?

— Reply to this email directly, view it on GitHubhttps://github.com/QFAB-Bioinformatics/metaDEGalaxy/issues/2, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AEX7CVTQXLA7NM5DVHHUBG3WB2G4TANCNFSM6AAAAAAQ6L2OXI. You are receiving this because you are subscribed to this thread.Message ID: @.***>

bernt-matthias commented 1 year ago

Thanks for the quick reply @mthang .. we will keep you posted.

paulzierep commented 1 year ago

We are also interested in these tools, and the complete WFs, excellent work. Mind if I (or rather one of our students) will start on porting them to IUC ? @mthang would you like to be involved, i.e. being asked to review the port ?

mthang commented 1 year ago

@paulzierep Not a problem. Please feel free to port them to IUC.

mthang commented 4 months ago

@bernt-matthias @paulzierep what do you think about this python program for converting the tabular files (i.e taxonomy.txt, metadata.txt and abundance.txt ) to phyloseq rds object. https://github.com/quadram-institute-bioscience/phylosequel . Perhaps, we can investigate this scripts and see if it suits our needs.

bernt-matthias commented 4 months ago

Looks good on a first glance, but I would wish that it is just the R script.

At least some of the checks in https://github.com/quadram-institute-bioscience/phylosequel/blob/main/scripts/phylosequel.py seem redundant with the checks in https://github.com/quadram-institute-bioscience/phylosequel/blob/main/phylosequel/phyloseq.R