Re: Something for MoM, outreachy? TODO for workflows Fwd: bcbio_1.1.3-1_amd64.changes ACCEPTED into unstable
Hi Stian,
On Fri, Mar 22, 2019 at 09:18:22AM +0000, Stian Soiland-Reyes wrote:
> On Thu, 2019-03-21 at 21:52 +0100, Andreas Tille wrote:
> > ChildIOException:
> > File/directory is a child to another output:
> > /home/andreas/debian-maintain/salsa/med-
> > team/0_prospective/kallisto/test/kallisto_out
> > /home/andreas/debian-maintain/salsa/med-
> > team/0_prospective/kallisto/test/kallisto_out/abundance.h5
> >
> >
> > I admit I never used snakemake and may be I'm doing something wrong.
> > But its not very good in telling the user what's wrong here. Any
> > hint?
>
> I guess we are talking about
> https://salsa.debian.org/med-team/kallisto/blob/master/test/Snakefile
That's correct.
> Try deleting the output "kallisto_out" in case it masks
> "kallisto_out/abundance.h5"
There is no such directory inside upstream tarball and thus not inside
the packaging directory since it was imported into the packaging
repository.
> or it might work simply marking it as directory("kallisto_out") as in
>
> https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#directories-as-outputs
I understand your hint as suggesting the following diff:
diff --git a/test/Snakefile b/test/Snakefile
index 1b2759c..382f763 100644
--- a/test/Snakefile
+++ b/test/Snakefile
@@ -6,6 +6,8 @@ INDEX = "{0}.kidx".format(PRE)
rule all:
input:
"kallisto_out/abundance.h5"
+ output:
+ directory("kallisto_out")
rule index:
input: FASTA
> You can then also try to change the overall output (aka all/input
> reqirements) to direcxtory("kallisto_out")
Unfortunately this did not change anything.
Thanks for your attempt to help in any case
Andreas.
--
http://fam-tille.de
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