Re: Too many hands on MultiQC Fwd: Bug#925304: Acknowledgement (ITP: multiqc -- output gathering for RNA sequencing across tools and samples)
On Sat, Mar 23, 2019 at 12:58:04AM +0100, Steffen Möller wrote:
>
> > I just commited my latest status.
> Modded and pushed back.
Cool.
> > The test suite is not running and
> > my attempt to fix it does not work. Good luck with it.
> On the command line it helped me to add the $(CURDIR)/.pybuild/... path
> to the module to PYTHONPATH but I also did not end anywhere. It is
> pretty close to uploadable, I think. The test, yes. I sense it to be a
> dh_auto_test incompatibility that I am not prepared to investigate at
> the moment. Instead, I am tempted to test it as part of a larger
> workflow for now and upload.
You can use it for the moment as local package. My impression
is that ftpmaster is not as quick as before the freeze. I see
chances that someone of our students might pick it up and I
usually ask on debian-python list. Trying this and upload in
7-10 days if there is no solution woul be no harm.
> >> I would otherwise fiddle with it here and there.
> > Your ITP bug would have profited if you would just have run
> > itp_from_debian_dir in the cloned dir. :-P
> I was actually looking for it. Twice :) Where do you hide that beast?
> Not even google knows. And neither does apt-cache search.
$ git log | tail
Author: Andreas Tille <tille@debian.org>
Date: Fri Mar 22 09:28:38 2019 +0100
Initial packaging
commit 4d90fbe076cc1e0b962891d8033940c070a46701
Author: Andreas Tille <tille@debian.org>
Date: Fri Mar 22 08:16:51 2019 +0100
New upstream version 1.7
I was about to send an ITP. We had a real racing condition.
> > PS: May be you can also have a look in to kallisto which just needs
> > to get a sensible test. Snakemake input is not working - extracting
> > the actual calls into a shell script could simplify things and does
> > not add an extra dependency from kallisto.
>
> I was impressed by what you have already done for the package. I am not
> available next week - I also suggest to commit it as it is if it is only
> for the test that is problematic. We are in a freeze anyway and I am
> more interested in seeing the different reverse dependencies finding
> that package so we get some first workflows done. And test the package
> with it, too.
I decided to extract the single shell commands snakemake would trigger.
There is no real point in creating an artificial snakemake dependency
just to call a few command lines. The first one seems to be
kallisto index -i transcripts.kidx transcripts.fasta.gz
kallisto quant -i transcripts.kidx -b 30 -o kallisto_out --genomebam --gtf transcripts.gtf.gz --chromosomes chrom.txt reads_1.fastq.gz reads_2.fastq.gz
which seems to be fine. However, before I messed up the command line and
had
kallisto quant -i transcripts.kidx -b 30 -o kallisto_out --genomebam --gtf transcripts.gtf.gz transcripts.fasta.gz --chromosomes reads_1.fastq.gz reads_2.fastq.gz
[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 14
[index] number of k-mers: 22,118
[index] number of equivalence classes: 20
Warning: could not find chromosomes for 117 transcripts
[quant] running in paired-end mode
[quant] will process pair 1: transcripts.fasta.gz
reads_2.fastq.gz
[quant] finding pseudoalignments for the reads ...Segmentation fault
Segmentation fault is not good!
I will check if I find some more tests and will report the
latest issue upstream.
Kind regards
Andreas.
--
http://fam-tille.de
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