bash external script: is it possibile to use it

[aborruso]

Hi,
I think it's not possible, but it would be great to use something like echo ${input[1]} in an external bash script.

Thank you for this great tool

[aborruso]

I must use mailing list, I'm closing it

[bricoletc]

Hi @aborruso , what came out of this? I'm quite keen on this feature too!

[aborruso]

hi @bricoletc this is for you https://groups.google.com/d/msg/snakemake/Nv9tzlgeqNE/KzoZro1yBQAJ

[bricoletc]

Thanks for your reply @aborruso !

I'm a little confused by that answer. Have you successfully called bash scripts from script directive inside a rule?

Here's what I get when running the following snakefile:

rule mkfiles:
	params:
		pref="test"
	script:
		"mkfiles.sh"

where the bash script contains:

for i in $(seq 1 5); do
	echo {snakemake.params.pref}$i
done

Stderr:

ValueError in line 5 of /path/to/tests/Snakefile:

Unsupported script: Expecting either Python (.py), R (.R), RMarkdown (.Rmd) or Julia (.jl) script.
  File "/path/to/tests/Snakefile", line 5, in __rule_mkfiles
  File "/usr/lib/python3.6/concurrent/futures/thread.py", line 56, in run

[aborruso]

I have not tested, I'm sorry. Please write a reply in the mailing list

…

______ Scusami per la brevità, ti sto scrivendo dal cellulare. website: https://medium.com/tantotanto 38° 7' 48" N, 13° 21' 9" E EPSG:4326 Il gio 16 apr 2020, 20:37 Brice Letcher <notifications@github.com> ha scritto:

Thanks for your reply @aborruso <https://github.com/aborruso> ! I'm a little confused by that answer. Have you successfully called bash scripts from script directive inside a rule? Here's what I get when running the following snakefile: rule mkfiles: params: pref="test" script: "mkfiles.sh" where the bash script contains: for i in $(seq 1 5); do echo {snakemake.params.pref}$i done Stderr: ValueError in line 5 of /path/to/tests/Snakefile: Unsupported script: Expecting either Python (.py), R (.R), RMarkdown (.Rmd) or Julia (.jl) script. File "/path/to/tests/Snakefile", line 5, in __rule_mkfiles File "/usr/lib/python3.6/concurrent/futures/thread.py", line 56, in run — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#294 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAHPDZ3T3ZJ4L2AZRCGAZLRM5F5RANCNFSM4LTULAFA> .

[bricoletc]

I think this is worth re-examining then.

Is lack of support for shell script because it is hard to implement, or for design reasons?

[mbhall88]

I think this is doable.

Since Bash v4, there are associative arrays, which are analogous to python dictionaries. There is a nice tutorial here showing how to work with these.

The main task for getting this working I expect is converting a python dictionary to a bash dictionary. I couldn't find any (obvious) existing libraries for this, but we could easily write a sublibrary within snakemake to do this conversion and then inject it into the bash script.

I'd be happy to dig into this once #1053 is merged (and provided @johanneskoester is happy to include such a feature).