Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

[Leonardo Collado Torres]

Thank you Andrzej for the info!


## Re-point (1)

Regarding my (1), I got my github repo in sync following
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
and 
http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
It all worked without problems. Thanks again for the great docs!


## on.bioc auto-detection

At 
https://github.com/LieberInstitute/recountWorkflow/commit/b456fbbe6ddbeda297ef03b79de9e004f28c0b97#diff-a87d0071c97357f224ad6608f837fbbfR45
I'm using

on.bioc <- knitr::opts_knit$get("rmarkdown.pandoc.to") != 'latex'

to detect automatically whether I'm rendering the output for Bioc or
not. For F1000 I'll use BiocWorkflowTools::f1000_article as the output
by calling rmarkdown::render() manually. I thought this little code
would help others who want to have a single repo for both BioC and
F1000.


## Re-point (5)

>From Lori's email that she sent today, I can see at
http://bioconductor.org/checkResults/3.7/workflows-LATEST/recountWorkflow/malbec2-buildwebvig.html
how the final Bioc web version is being built. That is:

/home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e
'rmarkdown::render(".buildwebvig/recountWorkflow/recount-workflow.Rmd",
output_format="BiocStyle:::html_fragment")' &&
/home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e
'knitr::purl(".buildwebvig/recountWorkflow/recount-workflow.Rmd",
".buildwebvig/recountWorkflow/recount-workflow.R")'

I can see the R version being used at
http://bioconductor.org/checkResults/3.7/workflows-LATEST/index.html
although not the bioc version (that I can infer from the package
loading messages, like clusterProfiler's one). This only matters in
those 6 months when release/devel are being built on the same R
version.

Now that I have the commands and versions, if I ever see anything
weird on the rendered Bioc web version I have a way to test things
myself instead of relying on the bioc builds. Since this is a bit
different than the rest of Bioc, maybe it'd be good to document the
build commands somewhere else.



Again, let me thank all of you for your work! I'm really excited about
the new workflow build chain and how it'll simplify
maintaining/writing workflows!


Best,
Leo

On Tue, Apr 3, 2018 at 6:38 AM, Andrzej Oleś  wrote:
>
> Dear Leo,
>
> thanks for you inquiry. Re points 2-4: there is no need to use the token file 
> .html_output anymore. This was an intermediate solution meant for the 
> transition period to new output format. Now all workflow vignettes for the 
> the website are build using this new format, regardless the `output` setting 
> in the vignette YAML header. Note that the format set in the vignette is 
> still used to render the document distributed with the package tarball.
>
> Cheers,
> Andrzej
>
>
> On Mon, Apr 2, 2018 at 4:32 PM, Leonardo Collado Torres  
> wrote:
>>
>> Hi,
>>
>> Thank you for all the work in this transition Andrzej, Lori, Valerie,
>> Nitesh and Hervé!
>>
>>
>> I have a few questions about the new system.
>>
>> 1) I already had a github repo (that I manually kept in sync with the
>> subversion one) for the recountWorkflow. Should I just follow the
>> instructions at
>> http://bioconductor.org/developers/how-to/git/sync-existing-repositories/?
>> I guess that I'll need to do this too
>> http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
>>
>> 2) Is repo/vignettes/.html_output still needed?
>>
>> 3) Related to (2), the .html_output file used to ignore the `output`
>> line in the vignette YAML. I got an email from Lori saying that
>> output: BiocWorkflowTools::f1000_article is not working for
>> recountWorfkflow for now (no html vignette). My guess is that the
>> `output` line now matters, and in my case, that would build a pdf file
>> which is ignored due to
>> https://github.com/LieberInstitute/recountWorkflow/blob/master/.Rbuildignore#L12
>> in my .Rbuildignore.
>>
>> 4) Related to the last 2. What setup do you recommend so I can
>> maintain a single git repo that produces the files needed for
>> uploading them to F1000research? Before this transition, I had to
>> maintain 3 repos: the subversion one for Bioc, my git copy (well,
>> main), and another one with the files setup for F1000. At some point
>> in the past, Andrzej recommended that I use "output:
>> BiocWorkflowTools::f1000_article" to try to have all the files in 1
>> place. I imagine that I would still need some ifelse() statements for
>> sentences like the one I have at
>> https://github.com/LieberInstitute/recountWorkflow/blob/master/vignettes/recount-workflow.Rmd#session-information
>> I think that this question could be generalized and documented in the
>> Bioc website.
>>
>> 5) Is there anything else I should be aware of so I can reproduce any
>> errors? In the past, the Bioc workflow system would trigger a build
>> immediately after a new push, and due to the custom way workflows were
>> built (like .html_output), I 

Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

[Aaron Lun]

It would also be nice to have a mechanism to obtain the underlying *.md
files used to generate the compiled workflow HTMLs. I've been using
this to check that the results have not changed since the last run.

Of course, I could also do this locally, but it would be reassuring to
confirm that the workflow is building correctly on the BioC machines.

-A

On Mon, 2018-04-02 at 11:42 +, Shepherd, Lori wrote:
> For now the page at 
> https://www.bioconductor.org/help/workflows/
> will remain and be updated accordingly however there is discussion
> about having this page be removed or redirected.  
> 
> In the next few days I hope to have the new landing pages up and
> running and will make an announcement when they are live. The new
> changes involve having a link to the workflows on the biocViews page,
> that will directly link to a workflow package landing page (like the
> software, annotation, and experiment package do). 
> 
> Until the release your changes will be visible in devel which will
> transition over to the new release just as done for software packages
> - 
> The workflow are built monday, wednesday, and friday and the new
> landing pages will reflect when the package is propagated like the
> other types of packages. 
> http://bioconductor.org/checkResults/3.7/workflows-LATEST/
> 
> Lori Shepherd
> Bioconductor Core Team
> Roswell Park Cancer Institute
> Department of Biostatistics & Bioinformatics
> Elm & Carlton Streets
> Buffalo, New York 14263
> From: Bioc-devel  on behalf of
> Aaron Lun 
> Sent: Sunday, April 1, 2018 2:17:09 PM
> To: Hervé Pagès; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] Workflows are now in git (and other
> Important workflow-related changes)
>  
> Thanks everybody, this is much appreciated.
> 
> On that note, will the compiled workflows shown at:
> 
> https://www.bioconductor.org/help/workflows/
> 
> ... be updated to reflect changes in the git repositories for the
> workflows? 
> 
> Or will the workflow page just directly link to the landing page for
> each package? This would be very convenient, not least because it
> will
> avoid me having to make pull requests to the bioconductor.org
> repository every time I want to change my workflow blurb.
> 
> I'm in the process of fixing and updating my various workflows, and
> I'm
> wondering when/how my changes will be visible to users.
> 
> Cheers,
> 
> Aaron
> 
> On Fri, 2018-03-30 at 13:10 -0700, Hervé Pagès wrote:
> > To the authors/maintainers of the workflows:
> > 
> > 
> > Following the svn-to-git migration of the software and data
> > experiment
> > packages last summer, we've completed the migration of the workflow
> > packages.
> > 
> > The canonical location for the workflow source code now is
> > git.bioconductor.org
> > 
> > Please use your git client to access/maintain your workflow the
> same
> > way you would do it for a software or data-experiment package.
> > 
> > We've also migrated the workflows to our in-house build system.
> > Starting with Bioc 3.7, the build report for the devel versions of
> > the workflows can be found here:
> > 
> >    https://bioconductor.org/checkResults/devel/workflows-LATEST/
> > 
> > We run these builds every other day (Mondays, Wednesdays, Fridays).
> > Because of limited build resources, we now run the data-experiment
> > builds on Sundays, Tuesdays, and Thursdays only (instead of daily).
> > 
> > The links to the package landing pages are not working yet. This
> > will be addressed in the next few days.
> > 
> > Please address any error you see on the report for the workflow
> > you maintain.
> > 
> > Note that, from now on, we're also following the same version
> scheme
> > for these packages as for the software and data-experiment
> packages.
> > That is, we're using an even y (in x.y.z) in release and an odd y
> in
> > devel. We'll take care of bumping y at release time (like we do for
> > software and data-experiment packages).
> > 
> > After the next Bioconductor release (scheduled for May 1), we'll
> > start
> > building the release versions of the workflows in addition to the
> > devel versions. The build report for the release versions will be
> > here:
> > 
> >    https://bioconductor.org/checkResults/release/workflows-LATEST/
> > 
> > Finally, please note that with the latest version of BiocInstaller
> > (1.29.5), workflow packages can be installed with biocLite(), like
> > any other Bioconductor package. We'll deprecate the old mechanism
> > (workflowInstall()) at some point in the future.
> > 
> > Thanks to Andrzej, Lori, Nitesh, and Valerie for working on this
> > migration.
> > 
> > Let us know if you have any question about this.
> > 
> > H.
> > 
> >
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> This email message may contain legally privileged and/or confidential
> information. If you are not 

Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

[Andrzej Oleś]

Dear Leo,

thanks for you inquiry. Re points 2-4: there is no need to use the token
file .html_output anymore. This was an intermediate solution meant for the
transition period to new output format. Now all workflow vignettes for the
the website are build using this new format, regardless the `output`
setting in the vignette YAML header. Note that the format set in the
vignette is still used to render the document distributed with the package
tarball.

Cheers,
Andrzej


On Mon, Apr 2, 2018 at 4:32 PM, Leonardo Collado Torres 
wrote:

> Hi,
>
> Thank you for all the work in this transition Andrzej, Lori, Valerie,
> Nitesh and Hervé!
>
>
> I have a few questions about the new system.
>
> 1) I already had a github repo (that I manually kept in sync with the
> subversion one) for the recountWorkflow. Should I just follow the
> instructions at
> http://bioconductor.org/developers/how-to/git/sync-existing-repositories/?
> I guess that I'll need to do this too
> http://bioconductor.org/developers/how-to/git/abandon-
> changes/#force-bioconductor--to-github-
>
> 2) Is repo/vignettes/.html_output still needed?
>
> 3) Related to (2), the .html_output file used to ignore the `output`
> line in the vignette YAML. I got an email from Lori saying that
> output: BiocWorkflowTools::f1000_article is not working for
> recountWorfkflow for now (no html vignette). My guess is that the
> `output` line now matters, and in my case, that would build a pdf file
> which is ignored due to
> https://github.com/LieberInstitute/recountWorkflow/blob/master/.
> Rbuildignore#L12
> in my .Rbuildignore.
>
> 4) Related to the last 2. What setup do you recommend so I can
> maintain a single git repo that produces the files needed for
> uploading them to F1000research? Before this transition, I had to
> maintain 3 repos: the subversion one for Bioc, my git copy (well,
> main), and another one with the files setup for F1000. At some point
> in the past, Andrzej recommended that I use "output:
> BiocWorkflowTools::f1000_article" to try to have all the files in 1
> place. I imagine that I would still need some ifelse() statements for
> sentences like the one I have at
> https://github.com/LieberInstitute/recountWorkflow/blob/master/
> vignettes/recount-workflow.Rmd#session-information
> I think that this question could be generalized and documented in the
> Bioc website.
>
> 5) Is there anything else I should be aware of so I can reproduce any
> errors? In the past, the Bioc workflow system would trigger a build
> immediately after a new push, and due to the custom way workflows were
> built (like .html_output), I relied on these builds to check if my
> changes had worked or not: specially early on where I had issues with
> figures, links to figures and figure captions.
>
> Best,
> Leo
>
>
>
>
>
>
> On Mon, Apr 2, 2018 at 7:42 AM, Shepherd, Lori
>  wrote:
> >
> > For now the page at
> >
> > https://www.bioconductor.org/help/workflows/
> >
> > will remain and be updated accordingly however there is discussion about
> having this page be removed or redirected.
> >
> >
> > In the next few days I hope to have the new landing pages up and running
> and will make an announcement when they are live. The new changes involve
> having a link to the workflows on the biocViews page, that will directly
> link to a workflow package landing page (like the software, annotation, and
> experiment package do).
> >
> >
> > Until the release your changes will be visible in devel which will
> transition over to the new release just as done for software packages -
> >
> > The workflow are built monday, wednesday, and friday and the new landing
> pages will reflect when the package is propagated like the other types of
> packages.
> > http://bioconductor.org/checkResults/3.7/workflows-LATEST/
> >
> >
> > Lori Shepherd
> >
> > Bioconductor Core Team
> >
> > Roswell Park Cancer Institute
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> >
> > 
> > From: Bioc-devel  on behalf of Aaron
> Lun 
> > Sent: Sunday, April 1, 2018 2:17:09 PM
> > To: Herv� Pag�s; bioc-devel@r-project.org
> > Subject: Re: [Bioc-devel] Workflows are now in git (and other Important
> workflow-related changes)
> >
> > Thanks everybody, this is much appreciated.
> >
> > On that note, will the compiled workflows shown at:
> >
> > https://www.bioconductor.org/help/workflows/
> >
> > ... be updated to reflect changes in the git repositories for the
> > workflows?
> >
> > Or will the workflow page just directly link to the landing page for
> > each package? This would be very convenient, not least because it will
> > avoid me having to make pull requests to the bioconductor.org
> > repository every time I want to change my workflow blurb.
> >
> > I'm in the process of fixing and updating my various workflows, 

Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

[Leonardo Collado Torres]

Hi,

Thank you for all the work in this transition Andrzej, Lori, Valerie,
Nitesh and Hervé!


I have a few questions about the new system.

1) I already had a github repo (that I manually kept in sync with the
subversion one) for the recountWorkflow. Should I just follow the
instructions at
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/?
I guess that I'll need to do this too
http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-

2) Is repo/vignettes/.html_output still needed?

3) Related to (2), the .html_output file used to ignore the `output`
line in the vignette YAML. I got an email from Lori saying that
output: BiocWorkflowTools::f1000_article is not working for
recountWorfkflow for now (no html vignette). My guess is that the
`output` line now matters, and in my case, that would build a pdf file
which is ignored due to
https://github.com/LieberInstitute/recountWorkflow/blob/master/.Rbuildignore#L12
in my .Rbuildignore.

4) Related to the last 2. What setup do you recommend so I can
maintain a single git repo that produces the files needed for
uploading them to F1000research? Before this transition, I had to
maintain 3 repos: the subversion one for Bioc, my git copy (well,
main), and another one with the files setup for F1000. At some point
in the past, Andrzej recommended that I use "output:
BiocWorkflowTools::f1000_article" to try to have all the files in 1
place. I imagine that I would still need some ifelse() statements for
sentences like the one I have at
https://github.com/LieberInstitute/recountWorkflow/blob/master/vignettes/recount-workflow.Rmd#session-information
I think that this question could be generalized and documented in the
Bioc website.

5) Is there anything else I should be aware of so I can reproduce any
errors? In the past, the Bioc workflow system would trigger a build
immediately after a new push, and due to the custom way workflows were
built (like .html_output), I relied on these builds to check if my
changes had worked or not: specially early on where I had issues with
figures, links to figures and figure captions.

Best,
Leo






On Mon, Apr 2, 2018 at 7:42 AM, Shepherd, Lori
 wrote:
>
> For now the page at
>
> https://www.bioconductor.org/help/workflows/
>
> will remain and be updated accordingly however there is discussion about 
> having this page be removed or redirected.
>
>
> In the next few days I hope to have the new landing pages up and running and 
> will make an announcement when they are live. The new changes involve having 
> a link to the workflows on the biocViews page, that will directly link to a 
> workflow package landing page (like the software, annotation, and experiment 
> package do).
>
>
> Until the release your changes will be visible in devel which will transition 
> over to the new release just as done for software packages -
>
> The workflow are built monday, wednesday, and friday and the new landing 
> pages will reflect when the package is propagated like the other types of 
> packages.
> http://bioconductor.org/checkResults/3.7/workflows-LATEST/
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> From: Bioc-devel  on behalf of Aaron Lun 
> 
> Sent: Sunday, April 1, 2018 2:17:09 PM
> To: Herv� Pag�s; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] Workflows are now in git (and other Important 
> workflow-related changes)
>
> Thanks everybody, this is much appreciated.
>
> On that note, will the compiled workflows shown at:
>
> https://www.bioconductor.org/help/workflows/
>
> ... be updated to reflect changes in the git repositories for the
> workflows?
>
> Or will the workflow page just directly link to the landing page for
> each package? This would be very convenient, not least because it will
> avoid me having to make pull requests to the bioconductor.org
> repository every time I want to change my workflow blurb.
>
> I'm in the process of fixing and updating my various workflows, and I'm
> wondering when/how my changes will be visible to users.
>
> Cheers,
>
> Aaron
>
> On Fri, 2018-03-30 at 13:10 -0700, Herv� Pag�s wrote:
> > To the authors/maintainers of the workflows:
> >
> >
> > Following the svn-to-git migration of the software and data
> > experiment
> > packages last summer, we've completed the migration of the workflow
> > packages.
> >
> > The canonical location for the workflow source code now is
> > git.bioconductor.org
> >
> > Please use your git client to access/maintain your workflow the same
> > way you would do it for a software or data-experiment package.
> >
> > We've also migrated the workflows to our in-house build system.
> > Starting with Bioc 3.7, the build report for the devel versions of
> > the 

Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

[Shepherd, Lori]

For now the page at

https://www.bioconductor.org/help/workflows/

will remain and be updated accordingly however there is discussion about having 
this page be removed or redirected.


In the next few days I hope to have the new landing pages up and running and 
will make an announcement when they are live. The new changes involve having a 
link to the workflows on the biocViews page, that will directly link to a 
workflow package landing page (like the software, annotation, and experiment 
package do).


Until the release your changes will be visible in devel which will transition 
over to the new release just as done for software packages -

The workflow are built monday, wednesday, and friday and the new landing pages 
will reflect when the package is propagated like the other types of packages.
http://bioconductor.org/checkResults/3.7/workflows-LATEST/


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Aaron Lun 

Sent: Sunday, April 1, 2018 2:17:09 PM
To: Herv� Pag�s; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Workflows are now in git (and other Important 
workflow-related changes)

Thanks everybody, this is much appreciated.

On that note, will the compiled workflows shown at:

https://www.bioconductor.org/help/workflows/

... be updated to reflect changes in the git repositories for the
workflows?

Or will the workflow page just directly link to the landing page for
each package? This would be very convenient, not least because it will
avoid me having to make pull requests to the bioconductor.org
repository every time I want to change my workflow blurb.

I'm in the process of fixing and updating my various workflows, and I'm
wondering when/how my changes will be visible to users.

Cheers,

Aaron

On Fri, 2018-03-30 at 13:10 -0700, Herv� Pag�s wrote:
> To the authors/maintainers of the workflows:
>
>
> Following the svn-to-git migration of the software and data
> experiment
> packages last summer, we've completed the migration of the workflow
> packages.
>
> The canonical location for the workflow source code now is
> git.bioconductor.org
>
> Please use your git client to access/maintain your workflow the same
> way you would do it for a software or data-experiment package.
>
> We've also migrated the workflows to our in-house build system.
> Starting with Bioc 3.7, the build report for the devel versions of
> the workflows can be found here:
>
>https://bioconductor.org/checkResults/devel/workflows-LATEST/
>
> We run these builds every other day (Mondays, Wednesdays, Fridays).
> Because of limited build resources, we now run the data-experiment
> builds on Sundays, Tuesdays, and Thursdays only (instead of daily).
>
> The links to the package landing pages are not working yet. This
> will be addressed in the next few days.
>
> Please address any error you see on the report for the workflow
> you maintain.
>
> Note that, from now on, we're also following the same version scheme
> for these packages as for the software and data-experiment packages.
> That is, we're using an even y (in x.y.z) in release and an odd y in
> devel. We'll take care of bumping y at release time (like we do for
> software and data-experiment packages).
>
> After the next Bioconductor release (scheduled for May 1), we'll
> start
> building the release versions of the workflows in addition to the
> devel versions. The build report for the release versions will be
> here:
>
>https://bioconductor.org/checkResults/release/workflows-LATEST/
>
> Finally, please note that with the latest version of BiocInstaller
> (1.29.5), workflow packages can be installed with biocLite(), like
> any other Bioconductor package. We'll deprecate the old mechanism
> (workflowInstall()) at some point in the future.
>
> Thanks to Andrzej, Lori, Nitesh, and Valerie for working on this
> migration.
>
> Let us know if you have any question about this.
>
> H.
>
>

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Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

[Aaron Lun]

Thanks everybody, this is much appreciated.

On that note, will the compiled workflows shown at:

https://www.bioconductor.org/help/workflows/

... be updated to reflect changes in the git repositories for the
workflows? 

Or will the workflow page just directly link to the landing page for
each package? This would be very convenient, not least because it will
avoid me having to make pull requests to the bioconductor.org
repository every time I want to change my workflow blurb.

I'm in the process of fixing and updating my various workflows, and I'm
wondering when/how my changes will be visible to users.

Cheers,

Aaron

On Fri, 2018-03-30 at 13:10 -0700, Hervé Pagès wrote:
> To the authors/maintainers of the workflows:
> 
> 
> Following the svn-to-git migration of the software and data
> experiment
> packages last summer, we've completed the migration of the workflow
> packages.
> 
> The canonical location for the workflow source code now is
> git.bioconductor.org
> 
> Please use your git client to access/maintain your workflow the same
> way you would do it for a software or data-experiment package.
> 
> We've also migrated the workflows to our in-house build system.
> Starting with Bioc 3.7, the build report for the devel versions of
> the workflows can be found here:
> 
>    https://bioconductor.org/checkResults/devel/workflows-LATEST/
> 
> We run these builds every other day (Mondays, Wednesdays, Fridays).
> Because of limited build resources, we now run the data-experiment
> builds on Sundays, Tuesdays, and Thursdays only (instead of daily).
> 
> The links to the package landing pages are not working yet. This
> will be addressed in the next few days.
> 
> Please address any error you see on the report for the workflow
> you maintain.
> 
> Note that, from now on, we're also following the same version scheme
> for these packages as for the software and data-experiment packages.
> That is, we're using an even y (in x.y.z) in release and an odd y in
> devel. We'll take care of bumping y at release time (like we do for
> software and data-experiment packages).
> 
> After the next Bioconductor release (scheduled for May 1), we'll
> start
> building the release versions of the workflows in addition to the
> devel versions. The build report for the release versions will be
> here:
> 
>    https://bioconductor.org/checkResults/release/workflows-LATEST/
> 
> Finally, please note that with the latest version of BiocInstaller
> (1.29.5), workflow packages can be installed with biocLite(), like
> any other Bioconductor package. We'll deprecate the old mechanism
> (workflowInstall()) at some point in the future.
> 
> Thanks to Andrzej, Lori, Nitesh, and Valerie for working on this
> migration.
> 
> Let us know if you have any question about this.
> 
> H.
> 
>

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Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

[Wolfgang Huber]

Thank you, Lori, Valerie, Andrzej, Nitesh and  Hervé, this is great 
news! This should help further rationalize the authoring and maintenance 
of workflows.



--
I'm sure many have also seen the call to submit workflows to the 
Bioconductor gateway on F1000Research 
https://support.bioconductor.org/p/107477/ - which will make your 
workflow a 'peer-reviewed' publication and gives it additional visibility.


 Best wishes
Wolfgang

30.3.18 22:10, Hervé Pagès scripsit:

To the authors/maintainers of the workflows:


Following the svn-to-git migration of the software and data experiment
packages last summer, we've completed the migration of the workflow
packages.

The canonical location for the workflow source code now is
git.bioconductor.org

Please use your git client to access/maintain your workflow the same
way you would do it for a software or data-experiment package.

We've also migrated the workflows to our in-house build system.
Starting with Bioc 3.7, the build report for the devel versions of
the workflows can be found here:

   https://bioconductor.org/checkResults/devel/workflows-LATEST/

We run these builds every other day (Mondays, Wednesdays, Fridays).
Because of limited build resources, we now run the data-experiment
builds on Sundays, Tuesdays, and Thursdays only (instead of daily).

The links to the package landing pages are not working yet. This
will be addressed in the next few days.

Please address any error you see on the report for the workflow
you maintain.

Note that, from now on, we're also following the same version scheme
for these packages as for the software and data-experiment packages.
That is, we're using an even y (in x.y.z) in release and an odd y in
devel. We'll take care of bumping y at release time (like we do for
software and data-experiment packages).

After the next Bioconductor release (scheduled for May 1), we'll start
building the release versions of the workflows in addition to the
devel versions. The build report for the release versions will be here:

   https://bioconductor.org/checkResults/release/workflows-LATEST/

Finally, please note that with the latest version of BiocInstaller
(1.29.5), workflow packages can be installed with biocLite(), like
any other Bioconductor package. We'll deprecate the old mechanism
(workflowInstall()) at some point in the future.

Thanks to Andrzej, Lori, Nitesh, and Valerie for working on this
migration.

Let us know if you have any question about this.

H.




--
With thanks in advance-
Wolfgang

---
Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany

wolfgang.hu...@embl.de
http://www.huber.embl.de

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