From: Nicholas Knoblauch <firstname.lastname@example.org> To: Kyle Meyer <email@example.com> Cc: firstname.lastname@example.org Subject: Re: [PATCH] mode: Add "container" and "envmodules" keywords Date: Sun, 1 Nov 2020 15:04:26 -0600 [thread overview] Message-ID: <D5A28139-EEF5-40D1-AF07-F2FAD0002645@gene.com> (raw) In-Reply-To: <email@example.com> > On Nov 1, 2020, at 2:36 PM, Kyle Meyer <firstname.lastname@example.org> wrote: > > Nicholas Knoblauch writes: > >> Hi, >> It would be great if snakemake-mode could support `envmodules` and >> `containers` as top level commands as per >> https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html?highlight=envmodules#using-environment-modules >> and >> https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html?highlight=envmodules#running-jobs-in-containers > > Sure, thanks for noticing that they're missing. Based on the docs, my > understanding is that "envmodules" can only be used within a rule: > > rule bwa: > envmodules: > "bio/bwa/0.7.9" > [...] > > On the other hand, it looks like "container" can be used either within a > rule or at the top-level. Is that correct? > I believe you’re right. >> Also, maybe I should file a separate issue about this (maybe it isn't even >> a snakemake-mode question), but is there a way to force the "rule" line to >> never indent (even if I hit 'Tab' on that line)? >> I consistently run into whitespace issues with org-mode+snakemake-mode. > > Hmm, not sure. Starting a separate thread with a minimal reproducer > would be great. Thanks. > Will do. Thanks again! > -- >8 -- > Subject: [PATCH] mode: Add "container" and "envmodules" keywords > > Register "container" as both a field key and a top-level command > because an example of both is present in the Snakemake docs. > > Reported-by: Nicholas Knoblauch <email@example.com> > --- > NEWS | 5 +++-- > snakemake-mode.el | 3 +++ > 2 files changed, 6 insertions(+), 2 deletions(-) > > diff --git a/NEWS b/NEWS > index f046551..2743025 100644 > --- a/NEWS > +++ b/NEWS > @@ -2,8 +2,9 @@ NEWS -- history of user-visible changes -*- mode: org; -*- > > * master (unreleased) > > -- Additional Snakemake keywords are now recognized: 'envvars' (new in > - Snakemake v5.11.0) and 'cache' keyword (new in v5.12.0). > +- Additional Snakemake keywords are now recognized: 'envmodules' (new > + in Snakemake v5.9.0), 'envvars' (new in v5.11.0), 'container' (new > + in v5.11.0), and 'cache' (new in v5.12.0). > > * v1.7.0 > > diff --git a/snakemake-mode.el b/snakemake-mode.el > index 5f603ee..cc4d372 100644 > --- a/snakemake-mode.el > +++ b/snakemake-mode.el > @@ -85,7 +85,9 @@ (eval-and-compile > (or "benchmark" > "cache" > "conda" > + "container" > "cwl" > + "envmodules" > "group" > "input" > "log" > @@ -110,6 +112,7 @@ (eval-and-compile > symbol-end)) > (sm-command . ,(rx symbol-start > (or "configfile" > + "container" > "envvars" > "include" > "localrules" > > base-commit: 870e1f2379110e48c7f189832aa7663fcb0be836 > -- > 2.28.0 >
next prev parent reply other threads:[~2020-11-01 21:04 UTC|newest] Thread overview: 4+ messages / expand[flat|nested] mbox.gz Atom feed top 2020-11-01 19:18 Add 'envmodules' and 'containers' to list of top level commands Nicholas Knoblauch 2020-11-01 20:36 ` [PATCH] mode: Add "container" and "envmodules" keywords Kyle Meyer 2020-11-01 21:04 ` Nicholas Knoblauch [this message] 2020-11-01 21:13 ` Kyle Meyer
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