A beta of bowtie2 has been released: http://bowtie-bio.sourceforge.net/bowtie2/ Any plans to either upgrade to this new version, or add a new package. If we wanted to keep the old one around, I see two possibilities. 1. create a new package "bowtie2" and keep "bowtie" at version 0.12.x 2. create a compatibility package "bowtie1" and update the current bowtie to bowtie2 I somewhat lean towards option (2). Of course if backwards compatibility is not desirable, then just option (3). 3. wait until bowtie2 becomes stable, and just update as normal.
Yes, I've been tracking bowtie2 and have made a start on a package. I think it best to keep the old one around, one way or the other. Any reason for preferring option (2)? I think I'd prefer (1), which seems to offer the least surprise.
(In reply to comment #1) > Yes, I've been tracking bowtie2 and have made a start on a package. I think it > best to keep the old one around, one way or the other. > > Any reason for preferring option (2)? I think I'd prefer (1), which seems to > offer the least surprise. I don't have a strong preference for (2), I figured it might be better in the long run if bowtie is the latest, and bowtie1 is the compatibility version, but in this case, perhaps better if we start with bowtie2 and once it becomes more standard than bowtie < 2, we can switch. Can we parallel install both? That would be ideal.
Taking this up again now - I need to update the original bowtie package as well as build the latest bowtie2 beta. Will look into making them parallel installable.
This bug appears to have been reported against 'rawhide' during the Fedora 19 development cycle. Changing version to '19'. (As we did not run this process for some time, it could affect also pre-Fedora 19 development cycle bugs. We are very sorry. It will help us with cleanup during Fedora 19 End Of Life. Thank you.) More information and reason for this action is here: https://fedoraproject.org/wiki/BugZappers/HouseKeeping/Fedora19
Created attachment 827148 [details] spec file for bowtie2 I've used the attached spec file for bowtie2. The binaries from the bowtie site distinguish bowtie and bowtie2, and Debian packages them both separately, so I did the same.
The latest bowtie2 builds bowtie binaries, but is restricted to 64-bit platforms. I've made an updated package, still called bowtie2, which maybe should change. It uses an unbundled libtinythread, which I assume is necessary: http://arc.liv.ac.uk/downloads/misc/SRPMS/bowtie2-2.2.3-1.el6.srpm http://arc.liv.ac.uk/downloads/misc/SRPMS/libtinythread++-1.1-1.el6.src.rpm I could put in a request for libtinythread if the bowtie2 package would be useful.
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This bug appears to have been reported against 'rawhide' during the Fedora 26 development cycle. Changing version to '26'.
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This bug appears to have been reported against 'rawhide' during the Fedora 29 development cycle. Changing version to '29'.
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This bug appears to have been reported against 'rawhide' during the Fedora 32 development cycle. Changing version to 32.
In review status at https://bugzilla.redhat.com/show_bug.cgi?id=1824348 .
As bowtie2 first build was just released to fedora rawhide (f33) now, I would close this ticket. Here is the dist-git repository. https://src.fedoraproject.org/rpms/bowtie2 To keep watching the release status for older Fedora (f32, f31, f30) and EPEL 8 and 7, you can subscribe the following ticket. https://bugzilla.redhat.com/show_bug.cgi?id=1824348