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Sat, 18 Feb 2023 04:21:59 -0500 (EST) From: Konrad Hinsen To: Simon Tournier , Guix Devel Subject: Re: Using Guix inside a Guix container In-Reply-To: <87a61c5mew.fsf@gmail.com> References: <87r0utize9.fsf@gmx.net> <87a61c5mew.fsf@gmail.com> Date: Sat, 18 Feb 2023 10:21:52 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Received-SPF: pass client-ip=66.111.4.27; envelope-from=konrad.hinsen@fastmail.net; helo=out3-smtp.messagingengine.com X-Spam_score_int: -27 X-Spam_score: -2.8 X-Spam_bar: -- X-Spam_report: (-2.8 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_LOW=-0.7, RCVD_IN_MSPIKE_H2=-0.001, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: guix-devel@gnu.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: X-Migadu-Queue-Id: 1E78D7598 X-Spam-Score: -1.63 X-Migadu-Spam-Score: -1.63 X-Migadu-Scanner: scn0.migadu.com List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+larch=yhetil.org@gnu.org Sender: guix-devel-bounces+larch=yhetil.org@gnu.org X-Migadu-Flow: FLOW_IN X-Migadu-Country: US X-TUID: 88O88jmrizKX Hi Simon, > Which part of Guix do you need inside the containerized shell that you > cannot do outside? That's not the right question. There's always a way to do what I want to do outside. But that may be very inconvenient. > Considering your use-case with Snakemake, what I am doing is to wrap > each rule with one containerized Guix shell which controls the > permissions, rule by rule; or a big containerized shell: > > guix shell -C -m manifest.scm --expose=3D=E2=80=A6 Nice example. I do the same: "guix shell" in every rule. Then I add stuff to my Snakefile, which is a Python script after all. For example, I import pandas to read a data frame from which I construct my workflow. Now I am at the point where I'd like to run snakemake itself in a container, to manage the dependencies of my Snakefile. In fact, given that I have workflows that depend on specific Snakemake versions, I'd really like to run Snakemake in a container all the time, even without additional dependencies. Without nested containers, I have to go through all the rules, collect the packages from their manifest files (or command line), and add them to the container in which I run the whole workflow. Possible, but not convenient. Another example: I run command-line programs from my Pharo image, and I have developed the habit of doing this always through Guix. The advantage is that my Pharo code becomes portable: it depends on Guix, but not on my profile. But if I want, one day, to move on to a full Guix system, I have to run Pharo in a container with LFS simulation. And then all my command line shell-outs will break. Both examples are about composing tools freely, without worrying if they use Guix internally or now. Cheers, Konrad