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List-Unsubscribe: , List-Archive: List-Post: X-Migadu-Queue-Id: 3DC23E1FC X-Spam-Score: -6.25 X-Migadu-Spam-Score: -6.25 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-Country: US X-Migadu-Flow: FLOW_IN X-TUID: g6CiiX5U7Swx ------ZEOR0F530DZ3U959OYM9Y711ETLGHH Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear Spencer,=20 I am a bit worried about your proposed project is too focused on replacing= python with guile=2E I think the project would benefit more from making py= thon users more comfortable productively using Guix tools in concert with t= he tools they are already comfortable with=2E I'm wondering if you might consider modifying your project goals toward ex= ploring how GWL might be enhanced so that it could better complement more e= xpressive language specific workflow tools like snakemake=2E I am also pers= onally interested in exploring such a facilities from the targets workflow = system in R as well=2E Alternatively, perhaps you could focus kn extending = the GWL with more features? I agree that establishing an achievable scope within a short timeline is c= rucial=2E The conda env importer idea would be quite an ambitious undertaki= ng by itself and would lead you towards thinking about some pretty interest= ing and impactful problems=2E On March 22, 2023 5:44:52 PM EDT, Spencer Skylar Chan wrote: >Hi Ricardo, > >On 3/22/23 14:19, Ricardo Wurmus wrote: >>=20 >>>> - Translating Snakemake to Guix Workflow Language (GWL) >>>=20 >>> Ricardo, maybe you would have some suggestions=2E :-) >>=20 >> Oh, this looks interesting=2E Could you please elaborate on the idea? >>=20 >My idea is to take as input a Snakemake workflow file and eventually outp= ut an equivalent GWL workflow file=2E > >Currently, Snakemake workflows can be exported to CWL (Common Workflow La= nguage): > >https://snakemake=2Ereadthedocs=2Eio/en/stable/executing/interoperability= =2Ehtml > >One approach could be to add CWL import/export capabilities to GWL=2E The= n Snakemake/GWL conversion would be a 2 step process, using CWL as an inter= mediate step: > >1=2E Snakemake -> CWL >2=2E CWL -> GWL > >However, CWL is not as expressive as Snakemake=2E There may be some detai= ls that are lost from Snakemake workflows=2E > >So a 1-step Snakemake/GWL transpiler could be interesting, as both Snakem= ake/GWL use a domain-specific language inside a general purpose language (P= ython/Guile respectively)=2E There may be a possibility to achieve more "ac= curate" translations between workflows=2E > >Is this topic something that could fit into a summer project? ------ZEOR0F530DZ3U959OYM9Y711ETLGHH Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear Spencer,

I am a bit worried about you= r proposed project is too focused on replacing python with guile=2E I think= the project would benefit more from making python users more comfortable p= roductively using Guix tools in concert with the tools they are already com= fortable with=2E

I'm wondering if you might consider modifying your = project goals toward exploring how GWL might be enhanced so that it could b= etter complement more expressive language specific workflow tools like snak= emake=2E I am also personally interested in exploring such a facilities fro= m the targets workflow system in R as well=2E Alternatively, perhaps you co= uld focus kn extending the GWL with more features?

I agree that esta= blishing an achievable scope within a short timeline is crucial=2E The cond= a env importer idea would be quite an ambitious undertaking by itself and w= ould lead you towards thinking about some pretty interesting and impactful = problems=2E


On March 22, 2023 5:44:52= PM EDT, Spencer Skylar Chan <schan12@terpmail=2Eumd=2Eedu> wrote: 
Hi Ricardo,

On 3/22/23 14:19, Ri=
cardo Wurmus wrote:
- Translating Snakemake to Guix Workflow Language (=
GWL)

Ricardo, maybe you would have some suggestions=2E =
:-)

Oh, this looks interesting=2E  Could you please ela=
borate on the idea?

My idea is to take as input a Snake=
make workflow file and eventually output an equivalent GWL workflow file=2E=


Currently, Snakemake workflows can be exported to CWL (Common Workf=
low Language):

https://snakemake=2Ereadthedocs=2Ei=
o/en/stable/executing/interoperability=2Ehtml

One approach could=
 be to add CWL import/export capabilities to GWL=2E Then Snakemake/GWL conv=
ersion would be a 2 step process, using CWL as an intermediate step:
1=2E Snakemake -> CWL
2=2E CWL -> GWL

However, CWL is not =
as expressive as Snakemake=2E There may be some details that are lost from =
Snakemake workflows=2E

So a 1-step Snakemake/GWL transpiler could be=
 interesting, as both Snakemake/GWL use a domain-specific language inside a=
 general purpose language (Python/Guile respectively)=2E There may be a pos=
sibility to achieve more "accurate" translations between workflows=2E
Is this topic something that could fit into a summer project?
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