| 22 Apr 2024 |
 pjotrp | Now git submodules | 10:35:26 |
 Andreas Tille | In reply to @pjotrp-linux:matrix.org
Is it possible we add the include files for fastahack and smithwaterman packages? That way I can unbundle those I admit I do not really understand. In Debian we have separate packages for vcflib, fastahack and smithwaterman. | 11:23:09 |
| pjotrp | Yes, but only binaries. No libs, no include filed | 14:55:38 |
| Andreas Tille | https://debconf24.debconf.org/talks/21-debian-med-bof/ | 16:17:23 |
 Charles Plessy | All my congratulations Andreas Tille! Will do my best to keep up with more uploads! | 23:35:36 |
| 23 Apr 2024 |
| Andreas Tille | That's the most welcome support I can imagine! | 04:30:56 |
| pjotrp | I fixed freebayes and it has a new release. By unbundling vcflib I had to bundle fastahack, smithwaterman and multichoose repos. They are all tiny. I still may need to add intervaltree. | 06:37:07 |
| Andreas Tille | Thanks a lot for your cooperation. If noone in the Debian Med team might step up, please ping again next week. I'm currently busy with DPL issues. | 07:42:30 |
 emollier | pjotrp: I have a look at freebayes, I see the new 1.3.8 and check whether it can be uploaded with the new version. | 19:43:03 |
| emollier | hm, i probably should have a look to see how to glue components back together. Taking the packaging straight, I get the following "configure/meson" error for the moment:
../meson.build:55.16: ERROR: File contrib/fastahack/Fasta.cpp does not exist. | 19:48:57 |
| emollier | because git submodules don't get pulled by uscan. | 19:58:19 |
| emollier | i drop the ball for this evening, I'm falling asleep. good night | 20:58:39 |
| 24 Apr 2024 |
| pjotrp | ah, right. Don't patch it please. I prefer to have these packages in a state that we don't have to look again :) | 02:21:56 |
| pjotrp | we have two routes. Create fastahack-dev that brings in a shared lib and include files - or I vendor this code (by the same author) into the main repo | 02:23:03 |
| pjotrp | or I make it part of libvcflib-dev. That can be the place we put this code as it is also used by vcflib. | 02:24:19 |
| pjotrp | my vgtools uses it. Let me check | 02:24:49 |
| pjotrp | oh wait, there is already libfasthack-dev. Let me incorporate that in freebayes | 02:28:10 |
| pjotrp | Andreas Tille: I now see what you mean. There is even libsmithwaterman-dev you wrote :) | 02:29:22 |
| pjotrp | excellent. I can unbundle | 02:29:37 |
| pjotrp | only libmultichoose-dev is missing | 02:31:18 |
| pjotrp | let me see if anyone is using that | 02:31:34 |
| pjotrp | vcflib of course | 02:31:55 |
| pjotrp | OK, there are some neglected PRs https://github.com/ekg/multichoose/pulls | 02:34:41 |
| pjotrp | that provided build/install commits ;) | 02:34:55 |
| pjotrp | so, do we want to create libmultichoose-dev? I can create a meson build, and we add that to Debian as a vcflib and freebayes dependency. Alternatively I pull the source code into vcflib. wdyt? | 02:36:05 |
| emollier | Hi pjotrp, if that helps, multichoose.h is already available from libvcflib-dev as /usr/include/vcflib/multichoose.h | 07:12:15 |
| emollier | but yeah, libmultichoose-dev would be of interest if you think it would be better to unbundle the header from the vcflib. | 07:14:30 |
| emollier | I had a quick look at multichoose source code, and it's short enough that I'm unsure about the overhead of dedicating a package if this is already bundled somewhere else. If you were to want to work on both vcflib and multichoose in a completely independent manner, a new multichoose-dev package would make sense though. | 07:16:25 |
| pjotrp | I'll take a look | 07:21:22 |
| emollier | ack, I'll do something else in the meantime. :) | 07:29:30 |
