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cgat-flow repository
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Conda Env for indexForSailfish error (libboost) #113

Closed jscaber closed 4 years ago

jscaber commented 4 years ago

The "sailfish" conda environment is also used for the function indexForSailfish. However indexForSailfish requires libboost=1.60.0, but on the "sailfish" conda environment it's 1.70.0 so it's throwing an error. Reverting back to the "cgat-flow" environment (libboost=1.66.0) appears to work.

sebastian-luna-valero commented 4 years ago

Many thanks, I will take a look asap.

jscaber commented 4 years ago

(it works up to a point - and then fails with an m-alloc error, but that is a problem with our cluster that is happening increasingly frequently)

Acribbs commented 4 years ago

Iv has earlier versions of salmon failing because of bad memory allocation on the cluster before. I think there was memory leaks on the cluster as this didn’t happen when I ran it locally. What’s your rationale sailfish and not salmon?

jscaber commented 4 years ago

No particular reason for sailfish other than it's part of this pipeline, and am trying to get it running again. Salmon works fine. I am just flagging this up, happy to close issue if no appetite in supporting the pipeline as it stands. Obviously no need to run sailfish and could be refactored towards salmon.

Acribbs commented 4 years ago

My preference would be to switch to salmon and remove sailfish. I like the pipeline and would continue to support it, but I dont have many RNA-seq datasets at the moment so I haven't used it for a while. I am happy to debug on my end when I have time (Maybe next week as im at a conference and some sessions dont look as interesting).

sebastian-luna-valero commented 4 years ago

Could you please confirm whether it's worth fixing the issue with sailfish then?

Acribbs commented 4 years ago

I personally think salmon is the way to go because sailfish isn't really supported anymore.

sebastian-luna-valero commented 4 years ago

Sailfish is being installed/used in its own conda environment:

https://github.com/cgat-developers/cgat-flow/blob/master/conda/environments/pipelines-sailfish.yml

Right now we use the latest available version but we could pin sailfish or its dependencies to ensure it works.

Do you want me to investigate further? Or are you finally getting rid of sailfish?

jscaber commented 4 years ago

Getting rid of sailfish. No need to support both, last sailfish release 2016. Jakub

On 13 Nov 2019, at 09:21, Sebastian Luna-Valero notifications@github.com<mailto:notifications@github.com> wrote:

Sailfish is being installed/used in its own conda environment:

https://github.com/cgat-developers/cgat-flow/blob/master/conda/environments/pipelines-sailfish.yml

Right now we use the latest available version but we could pin sailfish or its dependencies to ensure it works.

Do you want me to investigate further? Or are you finally getting rid of sailfish?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/cgat-developers/cgat-flow/issues/113?email_source=notifications&email_token=AC4Y5MVXNZHNSIEEL6Y44R3QTPBJTA5CNFSM4JKTU5YKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOED5OJNY#issuecomment-553313463, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AC4Y5MRMMCQ5MUSLG3I7JADQTPBJTANCNFSM4JKTU5YA.

sebastian-luna-valero commented 4 years ago

Thanks for confirming, Jakub.

Please bear in mind that getting rid of existing dependencies will help us reduce the number and complexity of conda environments, which is one of the bottlenecks of the continuous integration testing. If you guys are not comfortable modifying the conda environment, please feel free to ping me and I will happily look into that for you.

Best regards, Sebastian