On Fri, Feb 24, 2017 at 9:09 PM, Nitesh wrote:
> Could you tell me more about which package you are trying to wrap a recipe
> for?
>
Right now my packages: the recipes are working, but the helper skeleton
script that create dependencies gets them from DESCRIPTION and if lower
limits for version
I am trying to ease Bioconda recipes writers for Bioconductor packages.
The issue at hand is determining dependencies limits when one of the
packages that you depend on changes its public interface.
Up to now I admit that I did not fix my packages deps (adding a pin to a >=
version of them) when t
> We have been using snakemake (python-based, but essentially a domain
> language) with some pretty nice results. Nextflow (groovy-based) and Toil
> are another couple that I am watching closely. The Broad just released WDL
> and associated executors. And common-workflow-language (CWL) is gai
On Mon, Jun 20, 2016 at 11:36 AM, Sean Davis wrote:
> Hi, Elena.
>
> What do your pipelines need to do?
The idea behind our system is to be as general as possible. We are
mainly interested in human genomic/transcriptomic...we stem from
standard differential expression analyses
on microarray/RNAse
Hi,
TL;DR: what do you use to manage workflows and pipelines for you research? Knitr
or similar? Galaxy? Taverna?
Long version:
in my lab we are thinking about restyling our pipeline management
system and would like to exploit as much as possible the wealth of
annotations available in the Annota
On Fri, Jun 17, 2016 at 2:50 PM, Thomas Lin Pedersen
wrote:
> Thanks for that - for some reason it doesn’t create a local release-3.3
> branch that can be synced to svn? Anyway, I think it’s fair to say that there
> need to be some convenient way to update ones git environment after each
> Bioc
I manually added the tracking of the release branch picking some piece
of code from update_remotes.sh:
$ git config --add svn-remote.release-3.3.url
https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/PACKAGENAME
$ git config --add svn-remote.release-3.3.fetch
:refs/remotes/
On Wed, Jun 15, 2016 at 2:49 PM, Francesco Del Carratore
wrote:
> 2) Can somebody explain to me how to submit in the subversion control? I
> already looked in the Bioconductor website and I found it rather confusing
> (probably due to my poor English)
If you want we can talk off list in italian a
> Then I tried forking the repo available from bioconductor-mirror
> (https://github.com/Bioconductor-mirror/GenomicTuples). This resulted
> in an error due to a non-existent devel branch.
Yep, same here. I disabilited the git-svn bridge forked the
Bioconductor-mirror/REPO and cloned it, used upda
7;t really need to worry about the gory details of
> the changes. As I said earlier, things should be fixed and the
> build report back to "normal" before the end of the week.
>
> Thanks for your patience,
> H.
>
> >
> > All of the above said, SE was great and
Hi Hervé,
thanks for your kind answer - refactoring is always good, I've lagged
behind in the last months not following the novelties so to be
truthful it has been my fault and today I was in a bit of a hurry for
other reasons.
> I'm in the process of re-serializing
> RangedSummarizedExperiment o
Hello,
I'm writing as long as I am struggling a bit to keep the pace of
RangedSummarizedExperiment in my package roar, whose main class
contains RangedSummarizedExperiment to hold some of the data.
Sometimes the developers fix issues for me but I would like to ease
their work as much as possible b
Hi,
On Thu, Apr 9, 2015 at 10:27 AM, Ludwig Geistlinger
wrote:
> Error in file(con, "r") : cannot open the connection
> In addition: Warning message:
> In file(con, "r") : unable to resolve 'annotationhub.bioconductor.org'
That's strange, on linux it's working. Seems related to network
unavaila
I would guess that you need to add to the man page of the function in
the value section something like:
A named list with the following components:
\itemize{
\item \code{"p_pvalue"}: description of p_pvalue
\item \code{"p_tstat"}: description of p_tstat
}
HTH,
E.
--
$ pom
__
Hello,
I've just submitted a package and I'm trying to address the last
issues thanks to the automated building system (if it's inappropriate
to ask here before hearing from the reviewer please ignore this mail
and excuse me!).
I am still getting BUILD BIN warnings:
http://bioconductor.org/spb_re
Thank you both for your suggestions.
Peter: Rcpp attributes seem great but right now I would prefer to
avoid changing all the pure C structs of my old codebase in C++
classes and so on. But if in the future we will need to add new
features I will definitely add these two ++ :)
Dan: yep, that was r
Hi,
I'm writing a package that calculates total affinity (see PMID
21335606 and 16873464 if transcription factors are your thing):
up until now in our lab we've used a pure C tool that needs fasta and
tabular formatted PFM-PWM files but we are willing to produce
something more comfortable that ste
Yup, thank you very much: I had to link the dir to
/home/$USER/matrix_rider and it worked perfectly.
E.
--
$ pom
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Thank you very much, tomorrow I will apply this approach!
E.
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On Thu, Jan 8, 2015 at 4:43 PM, Dan Tenenbaum wrote:
>> I have a strange (ok, at least to me :) ) issue concerning volumes.
>> On a machine (debian testing/unstable up to date) everything works
>> smoothly when I do something like:
>> data@decoder:~$ docker run -v
>> /home/data/Dropbox/work/
>> ma
Thanks, this is really useful and I was looking forward to it after
having used rocker!
I have a strange (ok, at least to me :) ) issue concerning volumes.
On a machine (debian testing/unstable up to date) everything works
smoothly when I do something like:
data@decoder:~$ docker run -v
/home/data
s, therefore the ratio of these ratios
represents the relative "shortening" (or lengthening) in one condition
with respect to the other. As input, roar uses alignments files for
the two conditions and coordinates of the 3'UTRs with alternative
polyadenylation sites.
Any comment w
> You can use summarizeOverlaps with a 'BamFileList' created by something like
>
> myFiles = dir("/some/dir", pattern="bam$")
> bfl = BamFileList(myFiles, yieldSize=100)
> olaps = summarizeOverlaps(features, bfl)
>
> see the example on the help page
>
> method?"summarizeOverlaps,GRanges
Ok, thanks - I misread the manual, I just thought that was a way to
filter out reads falling over certain regions.
After reading the alignments I use summarizeOverlaps to obtain counts
with the desired options. I decided to use scanBamParam(which=..)
because loading bams and counting overlaps is us
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