Sounds good.
I should also mention that Rsamtools has pileup() that is available
on all platforms. Don't know how easy it would be to use to achieve
the kind of variant calling you're doing in MTseeker though...
Cheers,
H.
On 10/11/2018 04:35 AM, Tim Triche, Jr. wrote:
This makes sense. Windows users won’t be easily able to call variants across
thousands of samples but at least the plotting, impact prediction, etc will
work fine for them.
I will need to define things such that the variant calling is optional, which
is not too absurd — I’ll add loading of MVRanges/MVRangesList objects from VCFs
and move gmapR to suggests.
Personally I use the variant calling functionality regularly, but I have my
doubts as to whether someone on Windows would even have enough RAM to call
variants across 2000+ samples in a shot, so this is a good compromise.
Everything else is, I believe, platform agnostic. This should work.
--t
On Oct 11, 2018, at 1:41 AM, Hervé Pagès <hpa...@fredhutch.org> wrote:
And of course: the whole trick I described below only makes sense
if MTseeker doesn't rely on gmapR for its core functionality, that
is, if not having gmapR installed still allows the user to accomplish
something meaningful with MTseeker.
Otherwise the trick below will make MTseeker available on Windows
but Windows users won't be able to accomplish anything meaningful
with it. In that case, marking the package as unsupported on Windows
would be preferable.
Hope this makes sense,
H.
On 10/10/2018 10:26 PM, Hervé Pagès wrote:
Hi Tim,
No platform-specific dontrun capabilities AFAIK but you can use
something like:
if (requireNamespace("gmapR", quietly=TRUE)) {
...
...
}
in your man pages.
You would also need to move gmapR from Imports to Suggests.
Then make sure that MTseeker passes 'R CMD check' **without**
the gmapR package being installed. You'll need to define and set
environment variable _R_CHECK_FORCE_SUGGESTS_ to 0 for this.
Do it with:
export _R_CHECK_FORCE_SUGGESTS_=0
on Linux or Mac, or with:
set _R_CHECK_FORCE_SUGGESTS_=0
on Windows.
Once MTseeker is accepted, we'll add a .BBSoptions file with special
directive:
CHECKprepend.win: set _R_CHECK_FORCE_SUGGESTS_=0&&
This will have the effect to set the environment variable on the
Windows build machines before running 'R CMD check' there.
So MTseeker will be supported and available on all platforms.
For MTseekerData: the package doesn't seem to make any use of gmapR
so you can probably remove gmapR from its Suggests field.
Hope this helps,
H.
On 10/10/2018 07:46 AM, Tim Triche, Jr. wrote:
it looks like gmapR does not support Windows, and as a result, my MTseeker
package cannot build on tokay1, so the Data package which requires it also
cannot build on tokay1. Are there platform-specific dontrun capabilities?
https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_spb-5Freports_MTseekerData-5Fbuildreport-5F20181010103212.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=x8fxgyra6DmetOzKCh1Zm1X25BwPM7TDr8UUNYwgV18&s=QNKSsmQnfEAQOTI0r8dDuW_d01XzL_cL1cb5QIElLxw&e=
Short of somehow forcing gmapR to build on Windows, which I believe is
beyond my control, is there a way to declare that parts of the MTseeker
package are unsupported/unsupportable on Windows?
I suppose I could cleave off the variant-recalling portions but that seems
a little ridiculous. The original goal was to take the non-NuMT reads from
a given alignment, realign (only) those to rCRS/RSRS, and call against
that, for better mitochondrial haplogroup inference. We're still working
towards the full version, but even just calling variants against rCRS with
indels is hugely useful, and the ability to screen out haplogroup-specific
variants while retaining indels, SNVs, etc. turns out to be VERY handy.
More generally, there isn't any equivalent (AFAIK) in BioC, at all.
--t
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=x8fxgyra6DmetOzKCh1Zm1X25BwPM7TDr8UUNYwgV18&s=rzPUqLBge6xE1TymeYxIxJxkiiOHefbSgzPOLYEhvrM&e=
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
