aclum

spades program hangs when run with dmtcp_launch

16

Hi, I'm trying to run a bioinformatics program, spades and it hangs when I try to run it with dmctp_launch spades can be downloaded as a binary or as conda...

support for compressed fasta files

4

This is a feature request. It would be useful if FALCON supported commonly used compression formats for input files.

**Is your feature request related to a problem? Please describe.** [The quick install guide](https://linkml.io/linkml/intro/install.html) points to a docker container w/monarchinitiative as the org that that at first glance does not...

core file produced but final output is created

1

I'm assembling a ~20MB fungi on a 120 Gb node. The assembly completes successfully and looks reasonable but I'm getting a core file in the 3-asm stage. When I run...

update example data to napa -style identifiers

7

After re-iding is complete and the materialized pattern version of the schema is enforced some of the example data will fail validation because there are legacy style identifiers. We can...

Updates range of of was_informed_by to OmicsProcessing from Activity.

incorrect range for was_informed_by

15

WorkflowExecutionActivity subclasses populated was_informed_by with OmicsProcessing values. @picowatt pointed out that the specified range for was_informed_by is Activity and OmicsProcessing is a PlannedProcess, rooted in NamedThing, not under Activity. I'm...

Edit `FunctionalAnnotationAggMember ` to work with MetaP data

25

We added a nmdc schema Class for the gene aggregation for the sequencing workflows, see https://microbiomedata.github.io/nmdc-schema/FunctionalAnnotationAggMember/, but not for the metaproteomics. I believe we wanted all the collections in mongo...

Add RNA library permissible values to `LibraryTypeEnum` for `LibraryPreparation`'s `library_type` slot

5

Not urgent since it is not needed for NEON but we need a slot to capture the type of RNA library since this is needed input for Class MetatranscriptomeActivity Proposed...