Re: December: tophat
On 06.12.2017 16:20, Andreas Tille wrote: > Hi Fabian, > > On Wed, Dec 06, 2017 at 03:53:09PM +0100, Fabian Klötzl wrote: >> On 04.12.2017 17:33, Andreas Tille wrote: >>> >>> Thanks to the test suite we now know that the issue is not solved yet: >>> >>> $ sh run-unit-test >> >> That should be done with my recent commit; The new samtools version used >> a different set of arguments. > > I repackaged the upstream tarball to get really rid of the code copy and > did some according polishing as well. I also added a versioned > Dependency from samtools. It seems we need this versioning since if I > install the package on a stretch system the run-unit-test script fails. > Since we have samtools 1.3 on stretch it seems to be the reason for the > failure. I was testing on sid with samtools 1.5. So yeah, versioning seems like the way to go.
Re: December: tophat
Hi Fabian, On Wed, Dec 06, 2017 at 03:53:09PM +0100, Fabian Klötzl wrote: > On 04.12.2017 17:33, Andreas Tille wrote: > > > > Thanks to the test suite we now know that the issue is not solved yet: > > > > $ sh run-unit-test > > That should be done with my recent commit; The new samtools version used > a different set of arguments. I repackaged the upstream tarball to get really rid of the code copy and did some according polishing as well. I also added a versioned Dependency from samtools. It seems we need this versioning since if I install the package on a stretch system the run-unit-test script fails. Since we have samtools 1.3 on stretch it seems to be the reason for the failure. > That's an old one down for the advent calendar. ☺ That's a really nice one. :-) Please keep on with the bug squashing (as well as hopefully others will do!) Kind regards Andreas. -- http://fam-tille.de
Re: December: tophat
Hi Andreas, On 04.12.2017 17:33, Andreas Tille wrote: > On Mon, Dec 04, 2017 at 02:09:48PM +0100, Fabian Klötzl wrote: >> I just pushed some changes to build tophat with our version of libbam. >> Not sure if the previously mentioned issue in [1] is fixed; can't test, > > Thanks to the test suite we now know that the issue is not solved yet: > > $ sh run-unit-test That should be done with my recent commit; The new samtools version used a different set of arguments. That's an old one down for the advent calendar. ☺ Best Fabian
Re: [Debian-med-packaging] Bug#780816: December: tophat
On 04.12.2017 17:33, Andreas Tille wrote: > Thanks to the test suite we now know that the issue is not solved yet: > > $ sh run-unit-test > > [2017-12-04 17:28:54] Beginning TopHat run (v2.1.1) > --- > [2017-12-04 17:28:54] Checking for Bowtie > Bowtie version:2.3.3.1 > Error locating program: samtools_0.1.18 > > > Unfortunately a grep for this explicite string has several hits. I > have no idea what might happen if we replace it by /usr/bin/samtools. Ah, I took this as a build-only problem. Will look into it. Fabian
Re: December: tophat
Hi Fabian, thanks for working on this. On Mon, Dec 04, 2017 at 02:09:48PM +0100, Fabian Klötzl wrote: > I just pushed some changes to build tophat with our version of libbam. > Not sure if the previously mentioned issue in [1] is fixed; can't test, Thanks to the test suite we now know that the issue is not solved yet: $ sh run-unit-test [2017-12-04 17:28:54] Beginning TopHat run (v2.1.1) --- [2017-12-04 17:28:54] Checking for Bowtie Bowtie version:2.3.3.1 Error locating program: samtools_0.1.18 Unfortunately a grep for this explicite string has several hits. I have no idea what might happen if we replace it by /usr/bin/samtools. Kind regards Andreas. -- http://fam-tille.de
December: tophat
Hi all, I just pushed some changes to build tophat with our version of libbam. Not sure if the previously mentioned issue in [1] is fixed; can't test, because my cowbuild just broke. :( Best, Fabian [1]: https://lists.debian.org/debian-med/2014/10/msg4.html
