Requesting a tool integration

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Requesting a tool integration

Muhammet A. Celik
To whom may it concern;

We are writing to inquire on the possibility of contributing to the Galaxy
pool of tools.

At the outset, we thank the Galaxy community for all the hard work on the
wonderful platform, which is of a big value to the scientific community.

We are participants of the Open Life Science Project-2 (OLS-2) and are
mentored by Dr. Mallory Freeberg, who is also CCed in this email. Our
project is about creating a single pipeline integrating metagenomics tools
for taxonomic classification. The pipeline would ease the work of those
interested in metagenomic studies, especially those who do not have IT
background or enough computational resources. We also want to include a
visualization tool (Krona) to illustrate the output, since the standard
output is typically a txt file. The selected tools for the taxonomic
classification are Kraken2, Centrifuge and Clark, which are widely used and
identified as the state of the art based on our literature review.

Last week, we presented our work to Dr Berenice Batut (who is also CCed
herein), who is an expert in the field. Thanks to her feedback and advice
and that of Dr Mallory, we want to explore the prospect of porting our
project onto the Galaxy platform, to benefit the wider community. We have
checked both the Galaxy servers (https://usegalaxy.eu/ and
https://usegalaxy.org), as well as the ToolShed to see if the tools that we
want to deploy are already available on Galaxy.

Kraken2 is available and is ready for use with various DB's. On the other
hand, we were not able to find Centrifuge on the tools search section,
although it appears in the ToolShed (
https://toolshed.g2.bx.psu.edu/view/jvolkening/centrifuge/be7bba8229c6),
whereas Clark (http://clark.cs.ucr.edu/) is not available on the platform.

Thus, we hope that you could import these tools on Galaxy so that we can
port our pipeline(workflow) on the Galaxy platform.

Thank you,
Muhammet
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Re: Requesting a tool integration

Alex O
Muhammet,

I’d be happy to wrap Clark for you. Regarding putting Centrifuge, are you specifically trying to do this on a public instance such as usegalaxy.org <http://usegalaxy.org/> or use galaxy.eu <http://galaxy.eu/>, or would you prefer to perform the analysis locally? If you would like to to be on a public instance, please make an issue here: https://github.com/galaxyproject/usegalaxy-tools/issues <https://github.com/galaxyproject/usegalaxy-tools/issues> and mention which servers you are interested in using. We can get it up soon,

Thank you,
Alex Ostrovsky

> On Nov 16, 2020, at 9:28 PM, Muhammet A. Celik <[hidden email]> wrote:
>
> To whom may it concern;
>
> We are writing to inquire on the possibility of contributing to the Galaxy
> pool of tools.
>
> At the outset, we thank the Galaxy community for all the hard work on the
> wonderful platform, which is of a big value to the scientific community.
>
> We are participants of the Open Life Science Project-2 (OLS-2) and are
> mentored by Dr. Mallory Freeberg, who is also CCed in this email. Our
> project is about creating a single pipeline integrating metagenomics tools
> for taxonomic classification. The pipeline would ease the work of those
> interested in metagenomic studies, especially those who do not have IT
> background or enough computational resources. We also want to include a
> visualization tool (Krona) to illustrate the output, since the standard
> output is typically a txt file. The selected tools for the taxonomic
> classification are Kraken2, Centrifuge and Clark, which are widely used and
> identified as the state of the art based on our literature review.
>
> Last week, we presented our work to Dr Berenice Batut (who is also CCed
> herein), who is an expert in the field. Thanks to her feedback and advice
> and that of Dr Mallory, we want to explore the prospect of porting our
> project onto the Galaxy platform, to benefit the wider community. We have
> checked both the Galaxy servers (https://usegalaxy.eu/ and
> https://usegalaxy.org), as well as the ToolShed to see if the tools that we
> want to deploy are already available on Galaxy.
>
> Kraken2 is available and is ready for use with various DB's. On the other
> hand, we were not able to find Centrifuge on the tools search section,
> although it appears in the ToolShed (
> https://toolshed.g2.bx.psu.edu/view/jvolkening/centrifuge/be7bba8229c6),
> whereas Clark (http://clark.cs.ucr.edu/) is not available on the platform.
>
> Thus, we hope that you could import these tools on Galaxy so that we can
> port our pipeline(workflow) on the Galaxy platform.
>
> Thank you,
> Muhammet
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  %(web_page_url)s
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: Requesting a tool integration

Muhammet A. Celik
Dark Alex and Mallory,

I am happy to see your response, I must say it brightened my day. Thank you
so much, I appreciate your efforts. I will make the issue on the GitHub
page right away. Please accept my deepest thanks.

Best regards,
Muhammet

On Sat, Nov 21, 2020 at 1:21 AM Alex O <[hidden email]> wrote:

> Muhammet,
>
> I’d be happy to wrap Clark for you. Regarding putting Centrifuge, are you
> specifically trying to do this on a public instance such as usegalaxy.org or
> use galaxy.eu, or would you prefer to perform the analysis locally? If
> you would like to to be on a public instance, please make an issue here:
> https://github.com/galaxyproject/usegalaxy-tools/issues and mention which
> servers you are interested in using. We can get it up soon,
>
> Thank you,
> Alex Ostrovsky
>
> On Nov 16, 2020, at 9:28 PM, Muhammet A. Celik <[hidden email]>
> wrote:
>
> To whom may it concern;
>
> We are writing to inquire on the possibility of contributing to the Galaxy
> pool of tools.
>
> At the outset, we thank the Galaxy community for all the hard work on the
> wonderful platform, which is of a big value to the scientific community.
>
> We are participants of the Open Life Science Project-2 (OLS-2) and are
> mentored by Dr. Mallory Freeberg, who is also CCed in this email. Our
> project is about creating a single pipeline integrating metagenomics tools
> for taxonomic classification. The pipeline would ease the work of those
> interested in metagenomic studies, especially those who do not have IT
> background or enough computational resources. We also want to include a
> visualization tool (Krona) to illustrate the output, since the standard
> output is typically a txt file. The selected tools for the taxonomic
> classification are Kraken2, Centrifuge and Clark, which are widely used and
> identified as the state of the art based on our literature review.
>
> Last week, we presented our work to Dr Berenice Batut (who is also CCed
> herein), who is an expert in the field. Thanks to her feedback and advice
> and that of Dr Mallory, we want to explore the prospect of porting our
> project onto the Galaxy platform, to benefit the wider community. We have
> checked both the Galaxy servers (https://usegalaxy.eu/ and
> https://usegalaxy.org), as well as the ToolShed to see if the tools that
> we
> want to deploy are already available on Galaxy.
>
> Kraken2 is available and is ready for use with various DB's. On the other
> hand, we were not able to find Centrifuge on the tools search section,
> although it appears in the ToolShed (
> https://toolshed.g2.bx.psu.edu/view/jvolkening/centrifuge/be7bba8229c6),
> whereas Clark (http://clark.cs.ucr.edu/) is not available on the platform.
>
> Thus, we hope that you could import these tools on Galaxy so that we can
> port our pipeline(workflow) on the Galaxy platform.
>
> Thank you,
> Muhammet
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  %(web_page_url)s
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/
>
>
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  %(web_page_url)s

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/