[Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

[Neumann, Steffen]

Hi,

I would like to have a URL to individual files 
we have in BioC packages. This is useful 
e.g. if I need test data from, say, the msdata package,
in another context. 

In the SVN days, I was able to point directly 
into the SVN repo with readonly:readonly access. 
We also had the (now deprecated) way to link to:
https://raw.githubusercontent.com/Bioconductor-mirror/xcms/master/DESCRIPTION

-> Is there anything comparable today ?

It could be as simple as a directory tree 
of a working copies of all https://git.bioconductor.org/
served by the apache (or whatever) web server,
or (a bit cooler) a gitweb or similar http interface. 

Wouldn't that be a fantastic christmas present 
for us users and developers :-) ?

Yours,
Steffen

-- 

IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   http://msbi.bic-gh.de
06120 Halle  Tel. +49 (0) 345 5582 - 1470
  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
___
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Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

[Neumann, Steffen]

Hi,

this is a follow-up to a rather old thread, but with 
Mike Smith's (twitter: @grimbough) 

https://code.bioconductor.org/

We now have exactly what I had been looking for. 
Thanks Mike and BioC team !

Yours,
Steffen

On Mon, 2017-11-20 at 17:07 -0500, Martin Morgan wrote:
> On 11/20/2017 04:58 PM, Robert M. Flight wrote:
> > So, what if there was a MetaBioconductor site and repo similar to
> > the 
> > MetaCRAN project? https://www.r-pkg.org/about
> > 
> > Not sure exactly who maintains it (probably someone at RStudio),
> > but it 
> > is largely automatic I believe, and it provides a full GitHub
> > archive of 
> > *all* the packages on CRAN, which if this were done for
> > Bioconductor 
> > would satisfy what I think Steffen is looking for, as well as lots
> > of 
> > other advantages.
> > 
> > It also has the advantage that it looks like 90% of the work would
> > be 
> > done for Bioconductor with likely very little work required for
> > the 
> > Bioconductor Admins (ideally 100% of work would be done for them).
> 
> there has been some discussion of that, e.g.,
> 
>
> https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011455.html
> 
> but we will not do it (maintain a github mirror), for instance
> because 
> some experiment data packages have commits that would require lfs, 
> because of issues with reliably  syncing data, and because of
> confusion 
> it introduces on the 'official' repository.
> 
> We do intend to provide a browsable interface to the official 
> git.bioconductor.org that would allow Steffen's use case during the 
> present release cycle; it is not currently available.
> 
> A different solution would be to update the relevant ExperimentData 
> package to use ExperimentHub (see, e.g., 
> https://github.com/LTLA/TENxBrainData for a relatively simple
> example, 
> though not yet in Bioconductor) and the resource would then be
> available 
> at a URL https://annotationhub.bioconductor.org/fetch/...
> 
> Martin
> 
> > Just a thought.
> > 
> > -Robert
> > 
> > Robert M Flight, PhD
> > Bioinformatics Research Associate
> > Puller of Rabbits from Hats
> > Research Parasite
> > Resource Center for Stable Isotope Resolved Metabolomics
> > Manager, Systems Biology and Omics Integration Journal Club
> > Markey Cancer Center
> > CC434 Roach Building
> > University of Kentucky
> > Lexington, KY
> > 
> > Twitter: @rmflight
> > Web: rmflight.github.io 
> > ORCID: http://orcid.org/-0001-8141-7788
> > EM rfligh...@gmail.com 
> > PH 502-509-1827 
> > 
> > To call in the statistician after the experiment is done may be no
> > more 
> > than asking him to perform a post-mortem examination: he may be
> > able to 
> > say what the experiment died of. - Ronald Fisher
> > 
> > On Mon, Nov 20, 2017 at 8:51 AM Martin Morgan 
> >  > martin.mor...@roswellpark.org>> 
> > wrote:
> > 
> > On 11/19/2017 06:11 PM, Neumann, Steffen wrote:
> >  > Hi,
> >  >
> >  > thanks for the answer, unfortunately
> >  > not exactly what I meant. To be more precise:
> >  >
> >  > I want to point Galaxy to download (test) MS data files
> >  > from either the faahKO package, or msdata or mtbls2 in BioC.
> >  >
> >  > For that I need an ftp/http/https link to the files,
> >  > and I was able to use
> >  >
> >  >
> > 
> > https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/msdata/inst/cdf/ko15.CDF
> >  >
> >  > (which still works, but is probably outdated)
> >  > So is there anything equivalent in the new git setup ?
> > 
> > no, not from git.bioconductor.org 
> > ;.
> > 
> > Martin
> > 
> >  >
> >  > Yours,
> >  > Steffen
> >  >
> >  >
> >  > On Fri, 2017-11-17 at 04:31 -0500, Martin Morgan wrote:
> >  >> On 11/17/2017 04:08 AM, Neumann, Steffen wrote:
> >  >>> Hi,
> >  >>>
> >  >>> I would like to have a URL to individual files
> >  >>> we have in BioC packages. This is useful
> >  >>> e.g. if I need test data from, say, the msdata package,
> >  >>> in another context.
> >  >>>
> >  >>> In the SVN days, I was able to point directly
> >  >>> into the SVN repo with readonly:readonly access.
> >  >>> We also had the (now deprecated) way to link to:
> >  >>> 
> > https://raw.githubusercontent.com/Bioconductor-mirror/xcms/master/D
> >  >>> ESCRIPTION
> >  >>>
> >  >>> -> Is there anything comparable today ?
> >  >>
> >  >> I think the git archive command might do the trick, but it
> > requires
> >  >> ssh
> >  >> (i.e., write) access to the repository
> >  >>
> >  >> git archive --remote=g...@git.bioconductor.org:packages/xcms
> > \
> >  >>master DESCRIPTION | tar -xf -
> >  >>
> >  >>
> >  >>>
> >  >>> It could be as simple as a directory tree
> >  >>> of a working copies of all https://git.bioconductor.org/
>

Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

[Mike Smith]

Hi Steffen,

Thanks for the feedback.  I've been referencing this email thread when
presenting about developing the code website, so it might be old but it
wasn't forgotten!

Right now I think we still don't quite meet your use case, as
https://code.bioconductor.org/ currently only lists the software packages,
so msdata can't actually be found there.  That choice was because I had
limited disk-space in my prototypes of the site and so didn't try copying
any other type of package, but it doesn't have to remain that way.  I don't
know how much space might be needed for the other types of package, and
it's something I'm happy to consider for the future.

Cheers,
Mike

On Mon, 10 May 2021 at 09:10, Neumann, Steffen 
wrote:

> Hi,
>
> this is a follow-up to a rather old thread, but with
> Mike Smith's (twitter: @grimbough)
>
> https://code.bioconductor.org/
>
> We now have exactly what I had been looking for.
> Thanks Mike and BioC team !
>
> Yours,
> Steffen
>
> On Mon, 2017-11-20 at 17:07 -0500, Martin Morgan wrote:
> > On 11/20/2017 04:58 PM, Robert M. Flight wrote:
> > > So, what if there was a MetaBioconductor site and repo similar to
> > > the
> > > MetaCRAN project? https://www.r-pkg.org/about
> > >
> > > Not sure exactly who maintains it (probably someone at RStudio),
> > > but it
> > > is largely automatic I believe, and it provides a full GitHub
> > > archive of
> > > *all* the packages on CRAN, which if this were done for
> > > Bioconductor
> > > would satisfy what I think Steffen is looking for, as well as lots
> > > of
> > > other advantages.
> > >
> > > It also has the advantage that it looks like 90% of the work would
> > > be
> > > done for Bioconductor with likely very little work required for
> > > the
> > > Bioconductor Admins (ideally 100% of work would be done for them).
> >
> > there has been some discussion of that, e.g.,
> >
> >
> > https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011455.html
> >
> > but we will not do it (maintain a github mirror), for instance
> > because
> > some experiment data packages have commits that would require lfs,
> > because of issues with reliably  syncing data, and because of
> > confusion
> > it introduces on the 'official' repository.
> >
> > We do intend to provide a browsable interface to the official
> > git.bioconductor.org that would allow Steffen's use case during the
> > present release cycle; it is not currently available.
> >
> > A different solution would be to update the relevant ExperimentData
> > package to use ExperimentHub (see, e.g.,
> > https://github.com/LTLA/TENxBrainData for a relatively simple
> > example,
> > though not yet in Bioconductor) and the resource would then be
> > available
> > at a URL https://annotationhub.bioconductor.org/fetch/...
> >
> > Martin
> >
> > > Just a thought.
> > >
> > > -Robert
> > >
> > > Robert M Flight, PhD
> > > Bioinformatics Research Associate
> > > Puller of Rabbits from Hats
> > > Research Parasite
> > > Resource Center for Stable Isotope Resolved Metabolomics
> > > Manager, Systems Biology and Omics Integration Journal Club
> > > Markey Cancer Center
> > > CC434 Roach Building
> > > University of Kentucky
> > > Lexington, KY
> > >
> > > Twitter: @rmflight
> > > Web: rmflight.github.io 
> > > ORCID: http://orcid.org/-0001-8141-7788
> > > EM rfligh...@gmail.com 
> > > PH 502-509-1827 
> > >
> > > To call in the statistician after the experiment is done may be no
> > > more
> > > than asking him to perform a post-mortem examination: he may be
> > > able to
> > > say what the experiment died of. - Ronald Fisher
> > >
> > > On Mon, Nov 20, 2017 at 8:51 AM Martin Morgan
> > >  > > martin.mor...@roswellpark.org>>
> > > wrote:
> > >
> > > On 11/19/2017 06:11 PM, Neumann, Steffen wrote:
> > >  > Hi,
> > >  >
> > >  > thanks for the answer, unfortunately
> > >  > not exactly what I meant. To be more precise:
> > >  >
> > >  > I want to point Galaxy to download (test) MS data files
> > >  > from either the faahKO package, or msdata or mtbls2 in BioC.
> > >  >
> > >  > For that I need an ftp/http/https link to the files,
> > >  > and I was able to use
> > >  >
> > >  >
> > >
> > >
> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/msdata/inst/cdf/ko15.CDF
> > >  >
> > >  > (which still works, but is probably outdated)
> > >  > So is there anything equivalent in the new git setup ?
> > >
> > > no, not from git.bioconductor.org 
> > > ;.
> > >
> > > Martin
> > >
> > >  >
> > >  > Yours,
> > >  > Steffen
> > >  >
> > >  >
> > >  > On Fri, 2017-11-17 at 04:31 -0500, Martin Morgan wrote:
> > >  >> On 11/17/2017 04:08 AM, Neumann, Steffen wrote:
> > >  >>> Hi,
> > >  >>>
> > >  >>> I would like to have a URL to individual files
> > >  >>> we have in BioC packages. This is useful
> > >   

Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

[Martin Morgan]

The data/experiment and many data/annotation packages are not hosted in our git 
(!) so it would be necessary to take another approach (rsync + untar?) to 
obtaining their source.

Martin

On 5/10/21, 6:03 AM, "Bioc-devel on behalf of Mike Smith" 
 wrote:

Hi Steffen,

Thanks for the feedback.  I've been referencing this email thread when
presenting about developing the code website, so it might be old but it
wasn't forgotten!

Right now I think we still don't quite meet your use case, as
https://code.bioconductor.org/ currently only lists the software packages,
so msdata can't actually be found there.  That choice was because I had
limited disk-space in my prototypes of the site and so didn't try copying
any other type of package, but it doesn't have to remain that way.  I don't
know how much space might be needed for the other types of package, and
it's something I'm happy to consider for the future.

Cheers,
Mike

On Mon, 10 May 2021 at 09:10, Neumann, Steffen 
wrote:

> Hi,
>
> this is a follow-up to a rather old thread, but with
> Mike Smith's (twitter: @grimbough)
>
> https://code.bioconductor.org/
>
> We now have exactly what I had been looking for.
> Thanks Mike and BioC team !
>
> Yours,
> Steffen
>
> On Mon, 2017-11-20 at 17:07 -0500, Martin Morgan wrote:
> > On 11/20/2017 04:58 PM, Robert M. Flight wrote:
> > > So, what if there was a MetaBioconductor site and repo similar to
> > > the
> > > MetaCRAN project? https://www.r-pkg.org/about
> > >
> > > Not sure exactly who maintains it (probably someone at RStudio),
> > > but it
> > > is largely automatic I believe, and it provides a full GitHub
> > > archive of
> > > *all* the packages on CRAN, which if this were done for
> > > Bioconductor
> > > would satisfy what I think Steffen is looking for, as well as lots
> > > of
> > > other advantages.
> > >
> > > It also has the advantage that it looks like 90% of the work would
> > > be
> > > done for Bioconductor with likely very little work required for
> > > the
> > > Bioconductor Admins (ideally 100% of work would be done for them).
> >
> > there has been some discussion of that, e.g.,
> >
> >
> > https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011455.html
> >
> > but we will not do it (maintain a github mirror), for instance
> > because
> > some experiment data packages have commits that would require lfs,
> > because of issues with reliably  syncing data, and because of
> > confusion
> > it introduces on the 'official' repository.
> >
> > We do intend to provide a browsable interface to the official
> > git.bioconductor.org that would allow Steffen's use case during the
> > present release cycle; it is not currently available.
> >
> > A different solution would be to update the relevant ExperimentData
> > package to use ExperimentHub (see, e.g.,
> > https://github.com/LTLA/TENxBrainData for a relatively simple
> > example,
> > though not yet in Bioconductor) and the resource would then be
> > available
> > at a URL https://annotationhub.bioconductor.org/fetch/...
> >
> > Martin
> >
> > > Just a thought.
> > >
> > > -Robert
> > >
> > > Robert M Flight, PhD
> > > Bioinformatics Research Associate
> > > Puller of Rabbits from Hats
> > > Research Parasite
> > > Resource Center for Stable Isotope Resolved Metabolomics
> > > Manager, Systems Biology and Omics Integration Journal Club
> > > Markey Cancer Center
> > > CC434 Roach Building
> > > University of Kentucky
> > > Lexington, KY
> > >
> > > Twitter: @rmflight
> > > Web: rmflight.github.io 
> > > ORCID: http://orcid.org/-0001-8141-7788
> > > EM rfligh...@gmail.com 
> > > PH 502-509-1827 
> > >
> > > To call in the statistician after the experiment is done may be no
> > > more
> > > than asking him to perform a post-mortem examination: he may be
> > > able to
> > > say what the experiment died of. - Ronald Fisher
> > >
> > > On Mon, Nov 20, 2017 at 8:51 AM Martin Morgan
> > >  > > martin.mor...@roswellpark.org>>
> > > wrote:
> > >
> > > On 11/19/2017 06:11 PM, Neumann, Steffen wrote:
> > >  > Hi,
> > >  >
> > >  > thanks for the answer, unfortunately
> > >  > not exactly what I meant. To be more precise:
> > >  >
> > >  > I want to point Galaxy to download (test) MS data files
> > >  > from either the faahKO package, or msdata or mtbls2 in BioC.
> > >  >
> > >  > For that I need an ftp/http/https link to the files,
> > >  > and I was able to use
> > >  >
> 

Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

[Martin Morgan]

On 11/17/2017 04:08 AM, Neumann, Steffen wrote:

Hi,

I would like to have a URL to individual files
we have in BioC packages. This is useful
e.g. if I need test data from, say, the msdata package,
in another context.

In the SVN days, I was able to point directly
into the SVN repo with readonly:readonly access.
We also had the (now deprecated) way to link to:
https://raw.githubusercontent.com/Bioconductor-mirror/xcms/master/DESCRIPTION

-> Is there anything comparable today ?


I think the git archive command might do the trick, but it requires ssh 
(i.e., write) access to the repository


git archive --remote=g...@git.bioconductor.org:packages/xcms \
 master DESCRIPTION | tar -xf -




It could be as simple as a directory tree
of a working copies of all https://git.bioconductor.org/
served by the apache (or whatever) web server,
or (a bit cooler) a gitweb or similar http interface.

Wouldn't that be a fantastic christmas present
for us users and developers :-) ?

Yours,
Steffen




This email message may contain legally privileged and/or...{{dropped:2}}

___
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Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

[Neumann, Steffen]

Hi,

thanks for the answer, unfortunately 
not exactly what I meant. To be more precise:

I want to point Galaxy to download (test) MS data files 
from either the faahKO package, or msdata or mtbls2 in BioC.

For that I need an ftp/http/https link to the files,
and I was able to use 

https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/msdata/inst/cdf/ko15.CDF

(which still works, but is probably outdated)
So is there anything equivalent in the new git setup ?

Yours,
Steffen


On Fri, 2017-11-17 at 04:31 -0500, Martin Morgan wrote:
> On 11/17/2017 04:08 AM, Neumann, Steffen wrote:
> > Hi,
> > 
> > I would like to have a URL to individual files
> > we have in BioC packages. This is useful
> > e.g. if I need test data from, say, the msdata package,
> > in another context.
> > 
> > In the SVN days, I was able to point directly
> > into the SVN repo with readonly:readonly access.
> > We also had the (now deprecated) way to link to:
> > https://raw.githubusercontent.com/Bioconductor-mirror/xcms/master/D
> > ESCRIPTION
> > 
> > -> Is there anything comparable today ?
> 
> I think the git archive command might do the trick, but it requires
> ssh 
> (i.e., write) access to the repository
> 
> git archive --remote=g...@git.bioconductor.org:packages/xcms \
>   master DESCRIPTION | tar -xf -
> 
> 
> > 
> > It could be as simple as a directory tree
> > of a working copies of all https://git.bioconductor.org/
> > served by the apache (or whatever) web server,
> > or (a bit cooler) a gitweb or similar http interface.
> > 
> > Wouldn't that be a fantastic christmas present
> > for us users and developers :-) ?
> > 
> > Yours,
> > Steffen
> > 
> 
> 
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the
> employee or agent responsible for the delivery of this message to the
> intended recipient(s), you are hereby notified that any disclosure,
> copying, distribution, or use of this email message is
> prohibited.  If you have received this message in error, please
> notify the sender immediately by e-mail and delete this email message
> from your computer. Thank you.
-- 

IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   http://msbi.bic-gh.de
06120 Halle  Tel. +49 (0) 345 5582 - 1470
  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
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Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

[Martin Morgan]

On 11/19/2017 06:11 PM, Neumann, Steffen wrote:

Hi,

thanks for the answer, unfortunately
not exactly what I meant. To be more precise:

I want to point Galaxy to download (test) MS data files
from either the faahKO package, or msdata or mtbls2 in BioC.

For that I need an ftp/http/https link to the files,
and I was able to use

https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/msdata/inst/cdf/ko15.CDF

(which still works, but is probably outdated)
So is there anything equivalent in the new git setup ?


no, not from git.bioconductor.org.

Martin



Yours,
Steffen


On Fri, 2017-11-17 at 04:31 -0500, Martin Morgan wrote:

On 11/17/2017 04:08 AM, Neumann, Steffen wrote:

Hi,

I would like to have a URL to individual files
we have in BioC packages. This is useful
e.g. if I need test data from, say, the msdata package,
in another context.

In the SVN days, I was able to point directly
into the SVN repo with readonly:readonly access.
We also had the (now deprecated) way to link to:
https://raw.githubusercontent.com/Bioconductor-mirror/xcms/master/D
ESCRIPTION

-> Is there anything comparable today ?


I think the git archive command might do the trick, but it requires
ssh
(i.e., write) access to the repository

git archive --remote=g...@git.bioconductor.org:packages/xcms \
   master DESCRIPTION | tar -xf -




It could be as simple as a directory tree
of a working copies of all https://git.bioconductor.org/
served by the apache (or whatever) web server,
or (a bit cooler) a gitweb or similar http interface.

Wouldn't that be a fantastic christmas present
for us users and developers :-) ?

Yours,
Steffen




This email message may contain legally privileged and/or confidential
information.  If you are not the intended recipient(s), or the
employee or agent responsible for the delivery of this message to the
intended recipient(s), you are hereby notified that any disclosure,
copying, distribution, or use of this email message is
prohibited.  If you have received this message in error, please
notify the sender immediately by e-mail and delete this email message
from your computer. Thank you.



This email message may contain legally privileged and/or...{{dropped:2}}

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Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

[Robert M. Flight]

So, what if there was a MetaBioconductor site and repo similar to the
MetaCRAN project? https://www.r-pkg.org/about

Not sure exactly who maintains it (probably someone at RStudio), but it is
largely automatic I believe, and it provides a full GitHub archive of *all*
the packages on CRAN, which if this were done for Bioconductor would
satisfy what I think Steffen is looking for, as well as lots of other
advantages.

It also has the advantage that it looks like 90% of the work would be done
for Bioconductor with likely very little work required for the Bioconductor
Admins (ideally 100% of work would be done for them).

Just a thought.

-Robert

Robert M Flight, PhD
Bioinformatics Research Associate
Puller of Rabbits from Hats
Research Parasite
Resource Center for Stable Isotope Resolved Metabolomics
Manager, Systems Biology and Omics Integration Journal Club
Markey Cancer Center
CC434 Roach Building
University of Kentucky
Lexington, KY

Twitter: @rmflight
Web: rmflight.github.io
ORCID: http://orcid.org/-0001-8141-7788
EM rfligh...@gmail.com
PH 502-509-1827 <(502)%20509-1827>

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. - Ronald Fisher

On Mon, Nov 20, 2017 at 8:51 AM Martin Morgan 
wrote:

> On 11/19/2017 06:11 PM, Neumann, Steffen wrote:
> > Hi,
> >
> > thanks for the answer, unfortunately
> > not exactly what I meant. To be more precise:
> >
> > I want to point Galaxy to download (test) MS data files
> > from either the faahKO package, or msdata or mtbls2 in BioC.
> >
> > For that I need an ftp/http/https link to the files,
> > and I was able to use
> >
> >
> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/msdata/inst/cdf/ko15.CDF
> >
> > (which still works, but is probably outdated)
> > So is there anything equivalent in the new git setup ?
>
> no, not from git.bioconductor.org.
>
> Martin
>
> >
> > Yours,
> > Steffen
> >
> >
> > On Fri, 2017-11-17 at 04:31 -0500, Martin Morgan wrote:
> >> On 11/17/2017 04:08 AM, Neumann, Steffen wrote:
> >>> Hi,
> >>>
> >>> I would like to have a URL to individual files
> >>> we have in BioC packages. This is useful
> >>> e.g. if I need test data from, say, the msdata package,
> >>> in another context.
> >>>
> >>> In the SVN days, I was able to point directly
> >>> into the SVN repo with readonly:readonly access.
> >>> We also had the (now deprecated) way to link to:
> >>> https://raw.githubusercontent.com/Bioconductor-mirror/xcms/master/D
> >>> ESCRIPTION
> >>>
> >>> -> Is there anything comparable today ?
> >>
> >> I think the git archive command might do the trick, but it requires
> >> ssh
> >> (i.e., write) access to the repository
> >>
> >> git archive --remote=g...@git.bioconductor.org:packages/xcms \
> >>master DESCRIPTION | tar -xf -
> >>
> >>
> >>>
> >>> It could be as simple as a directory tree
> >>> of a working copies of all https://git.bioconductor.org/
> >>> served by the apache (or whatever) web server,
> >>> or (a bit cooler) a gitweb or similar http interface.
> >>>
> >>> Wouldn't that be a fantastic christmas present
> >>> for us users and developers :-) ?
> >>>
> >>> Yours,
> >>> Steffen
> >>>
> >>
> >>
> >> This email message may contain legally privileged and/or confidential
> >> information.  If you are not the intended recipient(s), or the
> >> employee or agent responsible for the delivery of this message to the
> >> intended recipient(s), you are hereby notified that any disclosure,
> >> copying, distribution, or use of this email message is
> >> prohibited.  If you have received this message in error, please
> >> notify the sender immediately by e-mail and delete this email message
> >> from your computer. Thank you.
>
>
> This email message may contain legally privileged and/or...{{dropped:2}}
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

[Robert M. Flight]

The other thing Steffen could do is keep personal clones of those packages
on GitHub, but that's probably not ideal.

-Robert

On Mon, Nov 20, 2017 at 4:58 PM Robert M. Flight 
wrote:

> So, what if there was a MetaBioconductor site and repo similar to the
> MetaCRAN project? https://www.r-pkg.org/about
>
> Not sure exactly who maintains it (probably someone at RStudio), but it is
> largely automatic I believe, and it provides a full GitHub archive of *all*
> the packages on CRAN, which if this were done for Bioconductor would
> satisfy what I think Steffen is looking for, as well as lots of other
> advantages.
>
> It also has the advantage that it looks like 90% of the work would be done
> for Bioconductor with likely very little work required for the Bioconductor
> Admins (ideally 100% of work would be done for them).
>
> Just a thought.
>
> -Robert
>
> Robert M Flight, PhD
> Bioinformatics Research Associate
> Puller of Rabbits from Hats
> Research Parasite
> Resource Center for Stable Isotope Resolved Metabolomics
> Manager, Systems Biology and Omics Integration Journal Club
> Markey Cancer Center
> CC434 Roach Building
> University of Kentucky
> Lexington, KY
>
> Twitter: @rmflight
> Web: rmflight.github.io
> ORCID: http://orcid.org/-0001-8141-7788
> EM rfligh...@gmail.com
> PH 502-509-1827 <(502)%20509-1827>
>
> To call in the statistician after the experiment is done may be no more
> than asking him to perform a post-mortem examination: he may be able to say
> what the experiment died of. - Ronald Fisher
>
> On Mon, Nov 20, 2017 at 8:51 AM Martin Morgan <
> martin.mor...@roswellpark.org> wrote:
>
>> On 11/19/2017 06:11 PM, Neumann, Steffen wrote:
>> > Hi,
>> >
>> > thanks for the answer, unfortunately
>> > not exactly what I meant. To be more precise:
>> >
>> > I want to point Galaxy to download (test) MS data files
>> > from either the faahKO package, or msdata or mtbls2 in BioC.
>> >
>> > For that I need an ftp/http/https link to the files,
>> > and I was able to use
>> >
>> >
>> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/msdata/inst/cdf/ko15.CDF
>> >
>> > (which still works, but is probably outdated)
>> > So is there anything equivalent in the new git setup ?
>>
>> no, not from git.bioconductor.org.
>>
>> Martin
>>
>> >
>> > Yours,
>> > Steffen
>> >
>> >
>> > On Fri, 2017-11-17 at 04:31 -0500, Martin Morgan wrote:
>> >> On 11/17/2017 04:08 AM, Neumann, Steffen wrote:
>> >>> Hi,
>> >>>
>> >>> I would like to have a URL to individual files
>> >>> we have in BioC packages. This is useful
>> >>> e.g. if I need test data from, say, the msdata package,
>> >>> in another context.
>> >>>
>> >>> In the SVN days, I was able to point directly
>> >>> into the SVN repo with readonly:readonly access.
>> >>> We also had the (now deprecated) way to link to:
>> >>> https://raw.githubusercontent.com/Bioconductor-mirror/xcms/master/D
>> >>> ESCRIPTION
>> >>>
>> >>> -> Is there anything comparable today ?
>> >>
>> >> I think the git archive command might do the trick, but it requires
>> >> ssh
>> >> (i.e., write) access to the repository
>> >>
>> >> git archive --remote=g...@git.bioconductor.org:packages/xcms \
>> >>master DESCRIPTION | tar -xf -
>> >>
>> >>
>> >>>
>> >>> It could be as simple as a directory tree
>> >>> of a working copies of all https://git.bioconductor.org/
>> >>> served by the apache (or whatever) web server,
>> >>> or (a bit cooler) a gitweb or similar http interface.
>> >>>
>> >>> Wouldn't that be a fantastic christmas present
>> >>> for us users and developers :-) ?
>> >>>
>> >>> Yours,
>> >>> Steffen
>> >>>
>> >>
>> >>
>> >> This email message may contain legally privileged and/or confidential
>> >> information.  If you are not the intended recipient(s), or the
>> >> employee or agent responsible for the delivery of this message to the
>> >> intended recipient(s), you are hereby notified that any disclosure,
>> >> copying, distribution, or use of this email message is
>> >> prohibited.  If you have received this message in error, please
>> >> notify the sender immediately by e-mail and delete this email message
>> >> from your computer. Thank you.
>>
>>
>> This email message may contain legally privileged and/or...{{dropped:2}}
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>

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Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

[Martin Morgan]

On 11/20/2017 04:58 PM, Robert M. Flight wrote:
So, what if there was a MetaBioconductor site and repo similar to the 
MetaCRAN project? https://www.r-pkg.org/about


Not sure exactly who maintains it (probably someone at RStudio), but it 
is largely automatic I believe, and it provides a full GitHub archive of 
*all* the packages on CRAN, which if this were done for Bioconductor 
would satisfy what I think Steffen is looking for, as well as lots of 
other advantages.


It also has the advantage that it looks like 90% of the work would be 
done for Bioconductor with likely very little work required for the 
Bioconductor Admins (ideally 100% of work would be done for them).


there has been some discussion of that, e.g.,

  https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011455.html

but we will not do it (maintain a github mirror), for instance because 
some experiment data packages have commits that would require lfs, 
because of issues with reliably  syncing data, and because of confusion 
it introduces on the 'official' repository.


We do intend to provide a browsable interface to the official 
git.bioconductor.org that would allow Steffen's use case during the 
present release cycle; it is not currently available.


A different solution would be to update the relevant ExperimentData 
package to use ExperimentHub (see, e.g., 
https://github.com/LTLA/TENxBrainData for a relatively simple example, 
though not yet in Bioconductor) and the resource would then be available 
at a URL https://annotationhub.bioconductor.org/fetch/...


Martin



Just a thought.

-Robert

Robert M Flight, PhD
Bioinformatics Research Associate
Puller of Rabbits from Hats
Research Parasite
Resource Center for Stable Isotope Resolved Metabolomics
Manager, Systems Biology and Omics Integration Journal Club
Markey Cancer Center
CC434 Roach Building
University of Kentucky
Lexington, KY

Twitter: @rmflight
Web: rmflight.github.io 
ORCID: http://orcid.org/-0001-8141-7788
EM rfligh...@gmail.com 
PH 502-509-1827 

To call in the statistician after the experiment is done may be no more 
than asking him to perform a post-mortem examination: he may be able to 
say what the experiment died of. - Ronald Fisher


On Mon, Nov 20, 2017 at 8:51 AM Martin Morgan 
mailto:martin.mor...@roswellpark.org>> 
wrote:


On 11/19/2017 06:11 PM, Neumann, Steffen wrote:
 > Hi,
 >
 > thanks for the answer, unfortunately
 > not exactly what I meant. To be more precise:
 >
 > I want to point Galaxy to download (test) MS data files
 > from either the faahKO package, or msdata or mtbls2 in BioC.
 >
 > For that I need an ftp/http/https link to the files,
 > and I was able to use
 >
 >

https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/msdata/inst/cdf/ko15.CDF
 >
 > (which still works, but is probably outdated)
 > So is there anything equivalent in the new git setup ?

no, not from git.bioconductor.org .

Martin

 >
 > Yours,
 > Steffen
 >
 >
 > On Fri, 2017-11-17 at 04:31 -0500, Martin Morgan wrote:
 >> On 11/17/2017 04:08 AM, Neumann, Steffen wrote:
 >>> Hi,
 >>>
 >>> I would like to have a URL to individual files
 >>> we have in BioC packages. This is useful
 >>> e.g. if I need test data from, say, the msdata package,
 >>> in another context.
 >>>
 >>> In the SVN days, I was able to point directly
 >>> into the SVN repo with readonly:readonly access.
 >>> We also had the (now deprecated) way to link to:
 >>> https://raw.githubusercontent.com/Bioconductor-mirror/xcms/master/D
 >>> ESCRIPTION
 >>>
 >>> -> Is there anything comparable today ?
 >>
 >> I think the git archive command might do the trick, but it requires
 >> ssh
 >> (i.e., write) access to the repository
 >>
 >> git archive --remote=g...@git.bioconductor.org:packages/xcms \
 >>    master DESCRIPTION | tar -xf -
 >>
 >>
 >>>
 >>> It could be as simple as a directory tree
 >>> of a working copies of all https://git.bioconductor.org/
 >>> served by the apache (or whatever) web server,
 >>> or (a bit cooler) a gitweb or similar http interface.
 >>>
 >>> Wouldn't that be a fantastic christmas present
 >>> for us users and developers :-) ?
 >>>
 >>> Yours,
 >>> Steffen
 >>>
 >>
 >>
 >> This email message may contain legally privileged and/or
confidential
 >> information.  If you are not the intended recipient(s), or the
 >> employee or agent responsible for the delivery of this message
to the
 >> intended recipient(s), you are hereby notified that any disclosure,
 >> copying, distribution, or use of this email message is
 >> prohibited.  If you have received this message in error, please
 >> notify the sender immediat

Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

[Robert M. Flight]

Right, in all this, I was forgetting the vast amount of confusion with the
Bioc GitHub mirror. I apologise.

Looking forward to having the web interface available.

Robert

On Mon, Nov 20, 2017, 17:08 Martin Morgan 
wrote:

> On 11/20/2017 04:58 PM, Robert M. Flight wrote:
> > So, what if there was a MetaBioconductor site and repo similar to the
> > MetaCRAN project? https://www.r-pkg.org/about
> >
> > Not sure exactly who maintains it (probably someone at RStudio), but it
> > is largely automatic I believe, and it provides a full GitHub archive of
> > *all* the packages on CRAN, which if this were done for Bioconductor
> > would satisfy what I think Steffen is looking for, as well as lots of
> > other advantages.
> >
> > It also has the advantage that it looks like 90% of the work would be
> > done for Bioconductor with likely very little work required for the
> > Bioconductor Admins (ideally 100% of work would be done for them).
>
> there has been some discussion of that, e.g.,
>
>https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011455.html
>
> but we will not do it (maintain a github mirror), for instance because
> some experiment data packages have commits that would require lfs,
> because of issues with reliably  syncing data, and because of confusion
> it introduces on the 'official' repository.
>
> We do intend to provide a browsable interface to the official
> git.bioconductor.org that would allow Steffen's use case during the
> present release cycle; it is not currently available.
>
> A different solution would be to update the relevant ExperimentData
> package to use ExperimentHub (see, e.g.,
> https://github.com/LTLA/TENxBrainData for a relatively simple example,
> though not yet in Bioconductor) and the resource would then be available
> at a URL https://annotationhub.bioconductor.org/fetch/...
>
> Martin
>
> >
> > Just a thought.
> >
> > -Robert
> >
> > Robert M Flight, PhD
> > Bioinformatics Research Associate
> > Puller of Rabbits from Hats
> > Research Parasite
> > Resource Center for Stable Isotope Resolved Metabolomics
> > Manager, Systems Biology and Omics Integration Journal Club
> > Markey Cancer Center
> > CC434 Roach Building
> > University of Kentucky
> > Lexington, KY
> >
> > Twitter: @rmflight
> > Web: rmflight.github.io 
> > ORCID: http://orcid.org/-0001-8141-7788
> > EM rfligh...@gmail.com 
> > PH 502-509-1827 
> >
> > To call in the statistician after the experiment is done may be no more
> > than asking him to perform a post-mortem examination: he may be able to
> > say what the experiment died of. - Ronald Fisher
> >
> > On Mon, Nov 20, 2017 at 8:51 AM Martin Morgan
> > mailto:martin.mor...@roswellpark.org>>
> > wrote:
> >
> > On 11/19/2017 06:11 PM, Neumann, Steffen wrote:
> >  > Hi,
> >  >
> >  > thanks for the answer, unfortunately
> >  > not exactly what I meant. To be more precise:
> >  >
> >  > I want to point Galaxy to download (test) MS data files
> >  > from either the faahKO package, or msdata or mtbls2 in BioC.
> >  >
> >  > For that I need an ftp/http/https link to the files,
> >  > and I was able to use
> >  >
> >  >
> >
> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/msdata/inst/cdf/ko15.CDF
> >  >
> >  > (which still works, but is probably outdated)
> >  > So is there anything equivalent in the new git setup ?
> >
> > no, not from git.bioconductor.org .
> >
> > Martin
> >
> >  >
> >  > Yours,
> >  > Steffen
> >  >
> >  >
> >  > On Fri, 2017-11-17 at 04:31 -0500, Martin Morgan wrote:
> >  >> On 11/17/2017 04:08 AM, Neumann, Steffen wrote:
> >  >>> Hi,
> >  >>>
> >  >>> I would like to have a URL to individual files
> >  >>> we have in BioC packages. This is useful
> >  >>> e.g. if I need test data from, say, the msdata package,
> >  >>> in another context.
> >  >>>
> >  >>> In the SVN days, I was able to point directly
> >  >>> into the SVN repo with readonly:readonly access.
> >  >>> We also had the (now deprecated) way to link to:
> >  >>>
> https://raw.githubusercontent.com/Bioconductor-mirror/xcms/master/D
> >  >>> ESCRIPTION
> >  >>>
> >  >>> -> Is there anything comparable today ?
> >  >>
> >  >> I think the git archive command might do the trick, but it
> requires
> >  >> ssh
> >  >> (i.e., write) access to the repository
> >  >>
> >  >> git archive --remote=g...@git.bioconductor.org:packages/xcms \
> >  >>master DESCRIPTION | tar -xf -
> >  >>
> >  >>
> >  >>>
> >  >>> It could be as simple as a directory tree
> >  >>> of a working copies of all https://git.bioconductor.org/
> >  >>> served by the apache (or whatever) web server,
> >  >>> or (a bit cooler) a gitweb or similar http interface.
> >  >>>
> >  >>> Wouldn't t

Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

[Neumann, Steffen]

Hi,

thanks everyone. In the short run I can certainly keep 
a personal copy, and in the long run Martin's solution 
will be exactly what I need, so no rush. 

Yours,
Steffen


On Mon, 2017-11-20 at 21:59 +, Robert M. Flight wrote:
> The other thing Steffen could do is keep personal clones of those
> packages on GitHub, but that's probably not ideal.
> 
> -Robert
> 
> On Mon, Nov 20, 2017 at 4:58 PM Robert M. Flight  > wrote:
> > So, what if there was a MetaBioconductor site and repo similar to
> > the MetaCRAN project? https://www.r-pkg.org/about
> > 
> > Not sure exactly who maintains it (probably someone at RStudio),
> > but it is largely automatic I believe, and it provides a full
> > GitHub archive of *all* the packages on CRAN, which if this were
> > done for Bioconductor would satisfy what I think Steffen is looking
> > for, as well as lots of other advantages. 
> > 
> > It also has the advantage that it looks like 90% of the work would
> > be done for Bioconductor with likely very little work required for
> > the Bioconductor Admins (ideally 100% of work would be done for
> > them).
> > 
> > Just a thought.
> > 
> > -Robert
> > 
> > Robert M Flight, PhD
> > Bioinformatics Research Associate
> > Puller of Rabbits from Hats
> > Research Parasite
> > Resource Center for Stable Isotope Resolved Metabolomics
> > Manager, Systems Biology and Omics Integration Journal Club
> > Markey Cancer Center
> > CC434 Roach Building
> > University of Kentucky
> > Lexington, KY
> > 
> > Twitter: @rmflight
> > Web: rmflight.github.io
> > ORCID: http://orcid.org/-0001-8141-7788
> > EM rfligh...@gmail.com
> > PH 502-509-1827
> > 
> > To call in the statistician after the experiment is done may be no
> > more than asking him to perform a post-mortem examination: he may
> > be able to say what the experiment died of. - Ronald Fisher
> > 
> > On Mon, Nov 20, 2017 at 8:51 AM Martin Morgan  > lpark.org> wrote:
> > > On 11/19/2017 06:11 PM, Neumann, Steffen wrote:
> > > > Hi,
> > > >
> > > > thanks for the answer, unfortunately
> > > > not exactly what I meant. To be more precise:
> > > >
> > > > I want to point Galaxy to download (test) MS data files
> > > > from either the faahKO package, or msdata or mtbls2 in BioC.
> > > >
> > > > For that I need an ftp/http/https link to the files,
> > > > and I was able to use
> > > >
> > > > https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/msda
> > > ta/inst/cdf/ko15.CDF
> > > >
> > > > (which still works, but is probably outdated)
> > > > So is there anything equivalent in the new git setup ?
> > > 
> > > no, not from git.bioconductor.org.
> > > 
> > > Martin
> > > 
> > > >
> > > > Yours,
> > > > Steffen
> > > >
> > > >
> > > > On Fri, 2017-11-17 at 04:31 -0500, Martin Morgan wrote:
> > > >> On 11/17/2017 04:08 AM, Neumann, Steffen wrote:
> > > >>> Hi,
> > > >>>
> > > >>> I would like to have a URL to individual files
> > > >>> we have in BioC packages. This is useful
> > > >>> e.g. if I need test data from, say, the msdata package,
> > > >>> in another context.
> > > >>>
> > > >>> In the SVN days, I was able to point directly
> > > >>> into the SVN repo with readonly:readonly access.
> > > >>> We also had the (now deprecated) way to link to:
> > > >>> https://raw.githubusercontent.com/Bioconductor-mirror/xcms/ma
> > > ster/D
> > > >>> ESCRIPTION
> > > >>>
> > > >>> -> Is there anything comparable today ?
> > > >>
> > > >> I think the git archive command might do the trick, but it
> > > requires
> > > >> ssh
> > > >> (i.e., write) access to the repository
> > > >>
> > > >> git archive --remote=g...@git.bioconductor.org:packages/xcms \
> > > >>    master DESCRIPTION | tar -xf -
> > > >>
> > > >>
> > > >>>
> > > >>> It could be as simple as a directory tree
> > > >>> of a working copies of all https://git.bioconductor.org/
> > > >>> served by the apache (or whatever) web server,
> > > >>> or (a bit cooler) a gitweb or similar http interface.
> > > >>>
> > > >>> Wouldn't that be a fantastic christmas present
> > > >>> for us users and developers :-) ?
> > > >>>
> > > >>> Yours,
> > > >>> Steffen
> > > >>>
> > > >>
> > > >>
> > > >> This email message may contain legally privileged and/or
> > > confidential
> > > >> information.  If you are not the intended recipient(s), or the
> > > >> employee or agent responsible for the delivery of this message
> > > to the
> > > >> intended recipient(s), you are hereby notified that any
> > > disclosure,
> > > >> copying, distribution, or use of this email message is
> > > >> prohibited.  If you have received this message in error,
> > > please
> > > >> notify the sender immediately by e-mail and delete this email
> > > message
> > > >> from your computer. Thank you.
> > > 
> > > 
> > > This email message may contain legally privileged
> > > and/or...{{dropped:2}}
> > > 
> > > ___
> > > Bioc-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
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