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dkim=pass header.d=elephly.net header.s=zoho header.b=L4gaoxxE; arc=pass ("zohomail.com:s=zohoarc:i=1"); dmarc=none; spf=pass (aspmx1.migadu.com: domain of "gwl-devel-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="gwl-devel-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: C1224FF47 X-Spam-Score: -9.75 X-Migadu-Scanner: scn0.migadu.com X-TUID: fFzhP9Nz6M0Q Hi Liliana, > I have a scientific workflow that depends on a bash script using an > extension. (I wish I did not.) Said script is the least common > denominator working on all systems that have some basic utilities, and > needs therefore not consider the reproducibility of its inputs (it is > assumed, that those are up to date). However, at least on my personal > machine I want to ensure the reproducibility of the entire workflow, > including the invocation of said script. > > I wrote a GWL workflow that calls the script, but due to the extension > the script actually fails in the GWL context. =C2=A0This is because GWL's > process->script unconditionally conses bash-minimal to the process > inputs. It should probably check whether a bash input already exists > or alternatively just append (list (bash-minimal)) instead. Would appending bash-minimal really help? Does it really give preference to your bash when resolving conflicts as it builds the profile? Not sure how we should check for the presence of a package providing a shell. We can check for certain packages by name, of course, but it doesn=E2=80=99t feel right to me. Any other ideas how to accommodate the need to swap out the package providing a shell? > For those in a similar situation as I am needing a fix, the following > works for me: instead of calling "bash" inside the workflow's inline > code, I specify > > values > run-with-store > open-connection > package-file bash "bin/bash" > > and use {{values}} instead of "bash" to call my script. (Don't forget > to add bash to your inputs, because package-file does not guarantee > existence of the file).=C2=A0 That=E2=80=99s an interesting solution. Thanks for sharing it. --=20 Ricardo