Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / koadman/proxigenomics issues and pull requests

#50 - Many scripts use "dumb" relative paths.

Issue - State: open - Opened by cerebis about 9 years ago

#49 - external binaries using path relative to invocation directory

Issue - State: open - Opened by cerebis about 9 years ago - 1 comment

#48 - design primers for carrier DNA

Issue - State: closed - Opened by koadman about 9 years ago - 1 comment

#47 - Simulation pipeline requires an overarching point of entry

Issue - State: open - Opened by cerebis over 9 years ago - 1 comment

#46 - Specify an overall output path

Issue - State: closed - Opened by cerebis over 9 years ago - 1 comment

#45 - External dependencies and overall structure a mess.

Issue - State: open - Opened by cerebis over 9 years ago

#43 - bam2edges and edges2metis should be combined.

Issue - State: open - Opened by cerebis over 9 years ago

#42 - reduce redundancy in job scripts

Issue - State: closed - Opened by koadman over 9 years ago - 2 comments

#41 - Scons/Nestly error

Issue - State: closed - Opened by koadman over 9 years ago - 2 comments

#40 - Ideally, our generated internal files should have annotation fields.

Issue - State: open - Opened by cerebis over 9 years ago - 1 comment

#38 - add support for running pipeline outside $HOME

Issue - State: open - Opened by koadman over 9 years ago

#37 - binaries required by mktree.sh are unavailable

Issue - State: open - Opened by koadman over 9 years ago - 2 comments

#36 - Support both Hi-C and meta3C read simulation

Issue - State: open - Opened by cerebis over 9 years ago

#35 - Large files and method of parsing BAM

Issue - State: open - Opened by cerebis over 9 years ago - 2 comments

#34 - contact_map.py memory usage

Issue - State: open - Opened by koadman over 9 years ago - 10 comments

#33 - weighted extended bcubed precision and recall

Issue - State: open - Opened by cerebis almost 10 years ago - 3 comments

#32 - code review pull request

Pull Request - State: open - Opened by koadman almost 10 years ago - 1 comment

#31 - Filesystem latency can cause rollbacks

Issue - State: closed - Opened by cerebis almost 10 years ago - 1 comment

#29 - Place basis sequences and trees somewhere sensible.

Issue - State: closed - Opened by cerebis almost 10 years ago

#28 - Externalize binaries path

Issue - State: closed - Opened by cerebis almost 10 years ago

#27 - Improve exit status propagation and rollback

Issue - State: closed - Opened by cerebis almost 10 years ago

#26 - Some alignment work is redundant.

Issue - State: closed - Opened by cerebis almost 10 years ago

#25 - Add assembly QA to pipeline.

Issue - State: closed - Opened by cerebis about 10 years ago - 1 comment

#24 - Glob on reference folder requires filter for files

Issue - State: closed - Opened by cerebis about 10 years ago - 2 comments

#23 - Share related parameters between make files

Issue - State: closed - Opened by cerebis about 10 years ago

#22 - simforward.py CLI help doesn't show reference and output paths.

Issue - State: closed - Opened by cerebis about 10 years ago

#21 - Place HPC logs into a log folder

Issue - State: closed - Opened by cerebis about 10 years ago

#20 - Pipeline path references require refactoring

Issue - State: open - Opened by cerebis about 10 years ago

#19 - Figure showing simulation workflow

Issue - State: closed - Opened by koadman about 10 years ago

#18 - Make pipeline runtime environment agnostic.

Issue - State: open - Opened by cerebis about 10 years ago - 2 comments

#17 - Integrate SG evolver

Issue - State: closed - Opened by cerebis about 10 years ago - 3 comments

#16 - Generated Fastq don't follow a naming convention

Issue - State: closed - Opened by cerebis almost 11 years ago - 1 comment
Labels: bug

#15 - Create SNP/mutational associations

Issue - State: closed - Opened by cerebis almost 11 years ago

#14 - Symmetric measures can be used as consensus tests

Issue - State: open - Opened by cerebis almost 11 years ago
Labels: enhancement, Clustering

#13 - Soft-clustering descriptive values

Issue - State: open - Opened by cerebis almost 11 years ago
Labels: enhancement, Clustering

#12 - Some code is running on the head node

Issue - State: open - Opened by cerebis almost 11 years ago
Labels: bug

#11 - Fix branching of pipeline developmental

Issue - State: closed - Opened by cerebis almost 11 years ago - 1 comment
Labels: bug

#10 - Soft-clustering

Issue - State: open - Opened by cerebis almost 11 years ago - 1 comment
Labels: enhancement, Clustering

#9 - Ground truth is only a guess

Issue - State: open - Opened by cerebis almost 11 years ago
Labels: enhancement, Clustering

#8 - Should performance metrics consider only classification

Issue - State: open - Opened by cerebis almost 11 years ago
Labels: enhancement, Clustering

#7 - Edge weighting

Issue - State: open - Opened by cerebis almost 11 years ago
Labels: enhancement, Clustering

#6 - Pruning of input graph

Issue - State: open - Opened by cerebis almost 11 years ago
Labels: enhancement, Clustering

#5 - The end-to-end workflow needs to be split into parts.

Issue - State: closed - Opened by cerebis almost 11 years ago - 3 comments
Labels: enhancement

#4 - User set random seed

Issue - State: closed - Opened by cerebis almost 11 years ago - 1 comment
Labels: enhancement

#3 - Write out community profile for simulation

Issue - State: closed - Opened by cerebis almost 11 years ago - 1 comment
Labels: enhancement, community definition

#2 - Community profile by specifying distribution function

Issue - State: open - Opened by cerebis almost 11 years ago - 1 comment
Labels: enhancement, community definition

#1 - Uniform community flag

Issue - State: open - Opened by cerebis almost 11 years ago - 1 comment
Labels: enhancement, community definition