Hello, science people,
Let me introduce myself. I am Jun Aruga. I am working for a ARM base bio genome analysis project as my side project with below ARM base HPC system (RHEL 7). I am interested in packaging some bio tools to install it on the environment. https://www.montblanc-project.eu/
First what I want to do is
* Updating samtools ( https://src.fedoraproject.org/rpms/samtools ) to latet version 1.9. * Adding new htslib RPM package with the sub package htslib-devel
The source as a reference. * samtools: https://github.com/samtools/samtools * htslib: https://github.com/samtools/htslib
On Debian, the samtools and htslib are available, I will refer the logic. https://packages.debian.org/sid/samtools
I am excited to join this community!
On Saturday, 10 August 2019 at 11:32, Jun Aruga wrote:
Hello, science people,
Let me introduce myself. I am Jun Aruga.
Welcome, Jun.
[...]
First what I want to do is
- Updating samtools ( https://src.fedoraproject.org/rpms/samtools ) to
latet version 1.9.
- Adding new htslib RPM package with the sub package htslib-devel
Great, let us know the review bug number once done. It's OK to post a work-in-progress version that doesn't even build if you need assistance with getting it to build.
Regards, Dominik
Jun Aruga jaruga@redhat.com writes:
First what I want to do is
- Updating samtools ( https://src.fedoraproject.org/rpms/samtools ) to
latet version 1.9.
- Adding new htslib RPM package with the sub package htslib-devel
You'll find (e.g. via https://fedoraproject.org/PackageReviewStatus/) there's already a stalled review for htslib: https://bugzilla.redhat.com/show_bug.cgi?id=1326504
Generally, also look on copr as well as bugzilla: https://copr.fedorainfracloud.org/coprs/fulltext/?fulltext=htslib
[I thought I had an htslib-based samtools in copr, but no.]
On Debian, the samtools and htslib are available, I will refer the logic. https://packages.debian.org/sid/samtools
While it's often worth referring to Debian packaging, you're probably better off starting with what the samtools maintainer already has in copr, especially as Debian packaging is rather simpler. There's also OpenSUSE (and the OBS equivalent of copr) which has a recent samtools, but OS spec files may need significant adjustment for Fedora.
For what it's worth, I'm starting to build some HPC packages for aarch64 in copr, including Extrae et al from the Mont Blanc stable.
Hi Dominik and Dave, thanks for the help and tips!
You'll find (e.g. via https://fedoraproject.org/PackageReviewStatus/) there's already a stalled review for htslib: https://bugzilla.redhat.com/show_bug.cgi?id=1326504
Sure I will keep in mind to check the current review status and Copr, and etc. I take a look at the ticket for htslib.
For what it's worth, I'm starting to build some HPC packages for aarch64 in copr, including Extrae et al from the Mont Blanc stable.
Oh thanks. Yes, Mont Blanc arch is aarch64.
You'll find (e.g. via https://fedoraproject.org/PackageReviewStatus/) there's already a stalled review for htslib: https://bugzilla.redhat.com/show_bug.cgi?id=1326504
Sure I will keep in mind to check the current review status and Copr, and etc. I take a look at the ticket for htslib.
For the htslib bugzilla ticket https://bugzilla.redhat.com/show_bug.cgi?id=1326504 I updated htslib.spec to the latest version 1.9, and commented on it. Is there any item to fix for the htslib.spec? Could you comment for the ticket ?
Thanks.
On Wed, Aug 14, 2019 at 11:17 AM Jun Aruga jaruga@redhat.com wrote:
Hi Dominik and Dave, thanks for the help and tips!
You'll find (e.g. via https://fedoraproject.org/PackageReviewStatus/) there's already a stalled review for htslib: https://bugzilla.redhat.com/show_bug.cgi?id=1326504
Sure I will keep in mind to check the current review status and Copr, and etc. I take a look at the ticket for htslib.
For what it's worth, I'm starting to build some HPC packages for aarch64 in copr, including Extrae et al from the Mont Blanc stable.
Oh thanks. Yes, Mont Blanc arch is aarch64.
-- Jun Aruga | He - His - Him
I wanted to post this again to let you know it. Here is the bug number of htslib that required by the latest samtools. https://bugzilla.redhat.com/show_bug.cgi?id=1326504
Thank you for the review!
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