Add Toil support back.

[DailyDreaming]

Referencing: #2710 @amizeranschi

@chapmanb Toil has been updated. Should I attempt to add it back into bcbio?

[chapmanb]

Lon;
Thanks so much for getting this up to date. I started working on getting the Toil package updated and I'm still hitting conflicts with the last released version of Toil and Arvados CWL runner. Arvados needs:

cwltool >=1.0.20181217162649
schema-salad >=3.0.20181129082112

and the 3.19.0 release pins to a version of cwltool and schemaSalad just prior:

cwltool = 'cwltool==1.0.20181118133959'
schemaSalad = 'schema-salad>=2.6, <3'

It looks like the current development version would work:

cwltool = 'cwltool==1.0.20190228155703'
schemaSalad = 'schema-salad<5,>=4.1'

Are there plans to have a new release soon and I could target an update of the conda packages to match this? Sorry for all the difficulties, it can be tricky to bring all of the CWL dependencies in sync. Thanks so much for the help.

[matthdsm]

Hi @chapmanb

It looks like Toil has already been bumped several versions since this issue. Could this be revisited?

Thanks
M

[chapmanb]

Matthias;
Thanks much for checking in on this. We'd be happy to accept patches if you'd like to investigate Toil support. Unfortunately I'm not close enough to it's development right now to be able to take this on, but happy to have you explore and see if you can get the packages in sync and get it working usefully for your needs. Sorry to not be able to help more.

[amizeranschi]

@roryk any chance of getting Toil support back into the main bcbio conda environmet by default? There's been a few new versions of it recently released on bioconda: https://anaconda.org/bioconda/toil

[fgvieira]

Dear all,

I've been trying to get toil to work with bcbio 1.2.3, but I am having some issues. Until now, I have just done:

conda install toil
conda install enlighten

Delete , "--linkImports" at https://github.com/bcbio/bcbio-nextgen/blob/master/bcbio/cwl/tool.py#L119

Change cwltoil to toil-cwl-runner at https://github.com/bcbio/bcbio-nextgen/blob/master/bcbio/cwl/tool.py#L129

But I am getting an error, and not sure why (since the file exists):

ERROR:cwltool:Got exception 'Not a file URI: /home/user/bed/regions.bed' while copying '/home/user/bed/regions.bed'

Anyone has any idea what it might be?
thanks,