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Re: Thanks for packaging golang-github-biogo-hts-dev - help for other biology related go package needed

(dropping pkg-go-maintainers@, since it's a legacy list which is
suppressed by debian-go@)

On Wed, Apr 17, 2019 at 7:28 PM Andreas Tille <andreas@an3as.eu> wrote:
> Hi Shengjing,
> by chance I realised that you have packaged biogo[1].  This is quite
> interesting for the Debian Med team and we have added the package to the
> "Biology development" task of our team[2] (since I now realised that the
> package exists in Debian).
> The goal of the Debian Med team is to provide simple and straightforward
> access to the package pool of Debian for users in life sciences and to
> advertise on a single entry point - the tasks pages and the according
> metapackage (in this case med-bio-dev) - all relevant packages.  Despite
> I'm observing the package pool quite closely this package escaped my
> attention until I now had a need for it and was explicitly seeking for
> it.
> In case there are more packages packaged by the golang team that would
> fit into any science (there are more Blends[3] than Debian Med and I'd
> volunteer to maintain the tasks files for other sciences) please let me
> know.

I don't think you should recommend user any golang-*-dev package.

Libraries written in Go are packaged for Debian with the only purpose
of building other Go programs for Debian. They are specifically not
available for users in their regular development workflow. For that,
users should use go get. [1]

> The actual problem I had was the packaging of vcfanno.  You can find
> my really poor attempt in Salsa[4].  I had never before touched a
> package written in go and I'd be happy to get some helping hand how
> to fix:
> ...
>    debian/rules override_dh_auto_build
> make[1]: Entering directory '/build/vcfanno-0.3.1'
> cp -a *.go obj-x86_64-linux-gnu
> dh_auto_build
> go: warning: "/..." matched no packages
>         cd obj-x86_64-linux-gnu && go install -gcflags=all=\"-trimpath=/build/vcfanno-0.3.1/obj-x86_64-linux-gnu/src\" -asmflags=all=\"-trimpath=/build/vcfanno-0.3.1/obj-x86_64-linux-gnu/src\" -v -p 4
> vcfanno.go:17:2: cannot find package "github.com/BurntSushi/toml" in any of:
>         /usr/lib/go-1.11/src/github.com/BurntSushi/toml (from $GOROOT)
>         /build/vcfanno-0.3.1/obj-x86_64-linux-gnu/src/github.com/BurntSushi/toml (from $GOPATH)

You could try the dh-make-golang[2], which could create debian package
for Go program.

For the vcfanno case, run
dh-make-golang make -type program -git_revision=v0.3.1 github.com/brentp/vcfanno

Then you could find some useful tips, like what build dependencies are
not packaged, and a near completed debian/ directory.

[1] https://go-team.pages.debian.net/packaging.html#_library_or_binary_library_packages
[2] https://packages.debian.org/sid/dh-make-golang

Shengjing Zhu

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