Re: CI for kraken

2017-08-07 Thread Andreas Tille
Hi Nadiya, On Mon, Aug 07, 2017 at 12:55:21PM -0700, Nadiya Sitdykova wrote: > 1. I don't know how to make it happen, maybe you can give some hints? > 2. I think I know the place where jellyfish is called, so it shouldn't be a > problem to patch kraken to use jellyfish1 Lets simply sit together l

Re: CI for kraken

2017-08-07 Thread Nadiya Sitdykova
Hello Andreas, 1. I don't know how to make it happen, maybe you can give some hints? 2. I think I know the place where jellyfish is called, so it shouldn't be a problem to patch kraken to use jellyfish1 Regards, Nadiya On Thu, Jul 20, 2017 at 9:30 PM, Andreas Tille wrote: > Hello Nadiya, > > O

CI for bamtools [Outreachy]

2017-08-07 Thread Nadiya Sitdykova
Hello Andreas, test-suite for bamtools package is ready. Regards, Nadiya

Re: [Help] Failed to upgrade bcftools to version 1.5

2017-08-07 Thread Graham Inggs
On 07/08/2017 17:49, Andreas Tille wrote: Do you think it would be sensible to file some RC bug against it to not enter testing? I cloned #871083 against python-pysam to #871314 and #871315 against htslib and samtools respectively.

Re: CI for trimmomatic

2017-08-07 Thread Nadiya Sitdykova
Hello Andreas, I added some info to README.source and renewed debian/copyright. Although I wasn't able to find authors of this experiment, only institution that submitted this data, so I wrote down the Fred Hutchinson Cancer Research Center as copyright. Is that ok? Regards, Nadiya On Fri, Jul 2

Re: [Help] Failed to upgrade bcftools to version 1.5

2017-08-07 Thread Andreas Tille
Hi, On Mon, Aug 07, 2017 at 11:05:22AM -0400, Afif Elghraoui wrote: > > Maybe RC bugs are a good idea. They probably should have been uploaded > to experimental Sorry for not beeing less carefully when I gave the green light to Matthias Klumpp for uploading his fix. I agree it should have been

Re: [Help] Failed to upgrade bcftools to version 1.5

2017-08-07 Thread Afif Elghraoui
Hi, Graham, [adding ticket log to Cc] على الإثنين 7 آب 2017 ‫10:40، كتب Graham Inggs: > Python-pysam 0.11.2.2+ds-3 migrated to testing on 2017-08-06, completing > the htslib/samtools/bcftools 1.4.1 transition. > > Now htslib 1.5-1 and samtools 1.5-1 have been uploaded and python-pysam > FTBFS

Re: [Help] Failed to upgrade bcftools to version 1.5

2017-08-07 Thread Graham Inggs
On 24/07/2017 06:12, Afif Elghraoui wrote: I was under the impression that htslib 1.5, required for bcftools 1.5, has a soname bump. There is no pysam release yet to wrap htslib 1.5, so I think upgrading bcftools/samtools/htslib right now to 1.5 will just make it impossible to use pysam until a n