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CPTR-ReSeqTB / UVP

Mycobacterium tuberculosis next generation sequence analysis
MIT License
21 stars 12 forks source link

Please produce a conda package #7

Closed tseemann closed 4 years ago

tseemann commented 5 years ago

Due to the number of dependences it would be great if you could package it for bioconda

See https://bioconda.github.io/

mezewudo commented 5 years ago

We will look into this for the next major revisions.

dfornika commented 5 years ago

I'm also interested in a bioconda package. I'm actually be interested in creating a Galaxy version of this workflow, but having all the pieces available in bioconda would be a good first step.

I noticed that fastQValidator is listed as a dependency but there is no bioconda package. With help from @npavlovikj we've been able to package fastQValidator's main dependency, libStatGen:

https://anaconda.org/bioconda/libstatgen

I have an open pull request to add fastQValidator but it seems to use a slightly non-standard build process, so it's a bit tricky to write the build.sh file:

https://github.com/bioconda/bioconda-recipes/pull/12319

The remaining dependencies all seem to be available on bioconda as far as I can tell.

d-yarmosh commented 5 years ago

Is the bioconda package available for others?

If not, is there a version of UVP capable of working with Kraken2? I am not sure I am able to find the older Kraken 0.10 version that is listed as a dependency and so I am attempting to modify the UVP source code to handle the difference in Kraken commands as well as results formatting (as needed).

mezewudo commented 5 years ago

The bioconda version is still work in progress, this version of UVP is tied to Kraken 0.10.

On Thu, Mar 28, 2019 at 2:20 PM David Yarmosh notifications@github.com wrote:

Is the bioconda package available for others?

If not, is there a version of UVP capable of working with Kraken2? I am not sure I am able to find the older Kraken 0.10 version that is listed as a dependency and so I am attempting to modify the UVP source code to handle the difference in Kraken commands as well as results formatting (as needed).

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dfornika commented 5 years ago

Hi @d-yarmosh. I have an open pull request here: #19 that will help prepare the project for bioconda packaging. I'll use @mezewudo 's test data to verify that the proposed changes won't affect the output or functionality of the pipeline. I hope to have a chance to do that this week.

d-yarmosh commented 5 years ago

Hi @dfornika, I don't suppose there's been an update? I continue to have trouble maintaining the assorted old versions of dependencies that UVP requires to run.

dfornika commented 5 years ago

Hello again @d-yarmosh. I apologize for not following up on this sooner. I've been busy with other work but this has been on my mind and I'll try to do the proposed test run as soon as possible so my PR can (hopefully) be merged.

But I'm curious, are you using conda to download dependencies? There are builds for kraken-0.10.5beta and kraken-0.10.6 available on bioconda:

https://anaconda.org/bioconda/kraken/files

Are those not appropriate?

d-yarmosh commented 5 years ago

Hi dfornika,

It's really a matter of doing this for every dependency, beyond just kraken. I'd been busy lately as well and was hoping for the easy one-command solution. Thanks for your help and good luck working this out! I'm sure it'a single install package will be a great benefit to all users.

On Thu, Apr 11, 2019 at 12:32 PM Dan Fornika notifications@github.com wrote:

Hello again @d-yarmosh https://github.com/d-yarmosh. I apologize for not following up on this sooner. I've been busy with other work but this has been on my mind and I'll try to do the proposed test run as soon as possible so my PR can (hopefully) be merged.

But I'm curious, are you using conda to download dependencies? There are builds for kraken-0.10.5beta and kraken-0.10.6 available on bioconda:

https://anaconda.org/bioconda/kraken/files

Are those not appropriate?

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dfornika commented 4 years ago

@d-yarmosh The master branch of UVP has been updated to improve portability and make installation a bit easier. The README.md file has been updated to include instructions for creating a conda environment that includes kraken and all other dependencies.

With these changes it should be possible to create a bioconda package soon.

d-yarmosh commented 4 years ago

Excellent news. Thanks for reaching out!

Dave

On Wed, Aug 14, 2019 at 2:10 PM Dan Fornika notifications@github.com wrote:

@d-yarmosh https://github.com/d-yarmosh The master branch of UVP has been updated to improve portability and make installation a bit easier. The README.md file has been updated to include instructions for creating a conda environment that includes kraken and all other dependencies.

With these changes it should be possible to create a bioconda package soon.

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dfornika commented 4 years ago

A conda package for UVP v2.6.0 has been published to the 'bioconda' channel:

https://anaconda.org/bioconda/uvp

Can this issue be closed?

d-yarmosh commented 4 years ago

Perfect, thank you. Please close this.

On Wed, Aug 28, 2019 at 2:06 PM Dan Fornika notifications@github.com wrote:

A conda package for UVP v2.6.0 has been published to the 'bioconda' channel:

https://anaconda.org/bioconda/uvp

Can this issue be closed?

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tseemann commented 4 years ago

Nice work @dfornika !