Ecosyste.ms: Issues

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

GitHub / cerebis/meta-sweeper issues and pull requests

#79 - A5 use of Unix "file" command is tricked by symbolic links

Issue - State: closed - Opened by cerebis over 7 years ago - 2 comments

#79 - A5 use of Unix "file" command is tricked by symbolic links

Issue - State: closed - Opened by cerebis over 7 years ago - 2 comments

#78 - Low coverage assemblies can return non-zero exit

Issue - State: open - Opened by cerebis over 7 years ago

#78 - Low coverage assemblies can return non-zero exit

Issue - State: open - Opened by cerebis over 7 years ago

#77 - More recent versions of Nextflow throw exceptions with MetaSweeper.java

Issue - State: closed - Opened by cerebis over 7 years ago - 1 comment

#77 - More recent versions of Nextflow throw exceptions with MetaSweeper.java

Issue - State: closed - Opened by cerebis over 7 years ago - 1 comment

#76 - Check sort order on contact_map.py

Issue - State: open - Opened by cerebis almost 8 years ago

#76 - Check sort order on contact_map.py

Issue - State: open - Opened by cerebis almost 8 years ago

#75 - Organisation of shared dependent modules

Issue - State: open - Opened by cerebis almost 8 years ago

#75 - Organisation of shared dependent modules

Issue - State: open - Opened by cerebis almost 8 years ago

#74 - Unintended rescaling of trans-rate

Issue - State: closed - Opened by cerebis almost 8 years ago

#74 - Unintended rescaling of trans-rate

Issue - State: closed - Opened by cerebis almost 8 years ago

#73 - Possible extension of profiles to include more definition.

Issue - State: open - Opened by cerebis almost 8 years ago

#73 - Possible extension of profiles to include more definition.

Issue - State: open - Opened by cerebis almost 8 years ago

#72 - Implement free shearing simulation

Issue - State: open - Opened by cerebis almost 8 years ago

#72 - Implement free shearing simulation

Issue - State: open - Opened by cerebis almost 8 years ago

#71 - Multi-chrom genomes with procedural abundances

Issue - State: open - Opened by cerebis about 8 years ago
Labels: enhancement, low priority

#71 - Multi-chrom genomes with procedural abundances

Issue - State: open - Opened by cerebis about 8 years ago
Labels: enhancement, low priority

#70 - Fine-tuning simple structure simulation by nested intervals

Issue - State: open - Opened by cerebis about 8 years ago - 1 comment

#70 - Fine-tuning simple structure simulation by nested intervals

Issue - State: open - Opened by cerebis about 8 years ago - 1 comment

#69 - Treatment of sparse sites and wgs read-pair noise

Issue - State: closed - Opened by cerebis about 8 years ago - 4 comments

#69 - Treatment of sparse sites and wgs read-pair noise

Issue - State: closed - Opened by cerebis about 8 years ago - 4 comments

#68 - Specifying a few resource limits might be useful.

Issue - State: open - Opened by cerebis about 8 years ago

#68 - Specifying a few resource limits might be useful.

Issue - State: open - Opened by cerebis about 8 years ago

#67 - Facility for fixed, user defined tree

Issue - State: closed - Opened by cerebis about 8 years ago - 2 comments

#67 - Facility for fixed, user defined tree

Issue - State: closed - Opened by cerebis about 8 years ago - 2 comments

#64 - snvbpnmft.py throws an error when there are no reliable variant sites.

Issue - State: closed - Opened by cerebis about 8 years ago
Labels: bug

#64 - snvbpnmft.py throws an error when there are no reliable variant sites.

Issue - State: closed - Opened by cerebis about 8 years ago
Labels: bug

#63 - Use of JavaSE8 Map.putIfAbsent()

Issue - State: open - Opened by cerebis about 8 years ago
Labels: low priority

#63 - Use of JavaSE8 Map.putIfAbsent()

Issue - State: open - Opened by cerebis about 8 years ago
Labels: low priority

#62 - nextflow hangs rather than exiting after workflow termination

Issue - State: open - Opened by koadman about 8 years ago - 3 comments
Labels: bug, nextflow related

#62 - nextflow hangs rather than exiting after workflow termination

Issue - State: open - Opened by koadman about 8 years ago - 3 comments
Labels: bug, nextflow related

#61 - params.debug undefined

Issue - State: closed - Opened by koadman about 8 years ago - 5 comments
Labels: bug, nextflow related

#61 - params.debug undefined

Issue - State: closed - Opened by koadman about 8 years ago - 5 comments
Labels: bug, nextflow related

#60 - Only two clades are used in multi-clade configurations

Issue - State: closed - Opened by koadman about 8 years ago
Labels: bug

#60 - Only two clades are used in multi-clade configurations

Issue - State: closed - Opened by koadman about 8 years ago
Labels: bug

#59 - Random sampling of parameter space

Issue - State: open - Opened by cerebis about 8 years ago - 1 comment
Labels: enhancement, high priority

#59 - Random sampling of parameter space

Issue - State: open - Opened by cerebis about 8 years ago - 1 comment
Labels: enhancement, high priority

#58 - pipeline_utils.py is not used

Issue - State: closed - Opened by cerebis about 8 years ago
Labels: low priority

#58 - pipeline_utils.py is not used

Issue - State: closed - Opened by cerebis about 8 years ago
Labels: low priority

#57 - bash_configure not setting environment variables

Issue - State: closed - Opened by koadman about 8 years ago - 3 comments
Labels: bug

#57 - bash_configure not setting environment variables

Issue - State: closed - Opened by koadman about 8 years ago - 3 comments
Labels: bug

#56 - Add documentation for satisfying beagle-lib dependency of timeseries workflow.

Issue - State: closed - Opened by cerebis over 8 years ago - 1 comment
Labels: enhancement

#56 - Add documentation for satisfying beagle-lib dependency of timeseries workflow.

Issue - State: closed - Opened by cerebis over 8 years ago - 1 comment
Labels: enhancement

#55 - wait_on jiffy only works for single files.

Issue - State: open - Opened by cerebis over 8 years ago

#55 - wait_on jiffy only works for single files.

Issue - State: open - Opened by cerebis over 8 years ago

#54 - test profile table no long correct format

Issue - State: closed - Opened by cerebis over 8 years ago

#54 - test profile table no long correct format

Issue - State: closed - Opened by cerebis over 8 years ago

#53 - JNI_LIB_PATH should not be an explicit absolute path

Issue - State: closed - Opened by cerebis over 8 years ago - 1 comment

#53 - JNI_LIB_PATH should not be an explicit absolute path

Issue - State: closed - Opened by cerebis over 8 years ago - 1 comment

#52 - sim3C: consider exposing more parameters controlling empirical distribution to users

Issue - State: open - Opened by cerebis over 8 years ago
Labels: enhancement, low priority

#52 - sim3C: consider exposing more parameters controlling empirical distribution to users

Issue - State: open - Opened by cerebis over 8 years ago
Labels: enhancement, low priority

#51 - 3-way channel cross in multisample

Issue - State: open - Opened by koadman over 8 years ago - 1 comment

#51 - 3-way channel cross in multisample

Issue - State: open - Opened by koadman over 8 years ago - 1 comment

#50 - Merge multisample into master

Issue - State: closed - Opened by koadman over 8 years ago

#50 - Merge multisample into master

Issue - State: closed - Opened by koadman over 8 years ago

#49 - Validate poly-chromosomal genomes in sim3C

Issue - State: closed - Opened by cerebis over 8 years ago - 1 comment

#49 - Validate poly-chromosomal genomes in sim3C

Issue - State: closed - Opened by cerebis over 8 years ago - 1 comment

#48 - Validate treatment of sim3C site duplication

Issue - State: closed - Opened by cerebis over 8 years ago - 2 comments

#48 - Validate treatment of sim3C site duplication

Issue - State: closed - Opened by cerebis over 8 years ago - 2 comments

#47 - Adopt a space efficient graph interchange format

Issue - State: open - Opened by cerebis over 8 years ago - 4 comments
Labels: enhancement, low priority

#47 - Adopt a space efficient graph interchange format

Issue - State: open - Opened by cerebis over 8 years ago - 4 comments
Labels: enhancement, low priority

#46 - Some naive operations possess poor time complexity.

Issue - State: closed - Opened by cerebis over 8 years ago
Labels: low priority

#46 - Some naive operations possess poor time complexity.

Issue - State: closed - Opened by cerebis over 8 years ago
Labels: low priority

#45 - Longer read-pairs (250bp) can lead to read-through problems. Add a warning.

Issue - State: closed - Opened by cerebis over 8 years ago - 5 comments
Labels: enhancement, low priority

#45 - Longer read-pairs (250bp) can lead to read-through problems. Add a warning.

Issue - State: closed - Opened by cerebis over 8 years ago - 5 comments
Labels: enhancement, low priority

#44 - Read creation rate of ART could be improved.

Issue - State: closed - Opened by cerebis over 8 years ago - 1 comment
Labels: enhancement, low priority

#44 - Read creation rate of ART could be improved.

Issue - State: closed - Opened by cerebis over 8 years ago - 1 comment
Labels: enhancement, low priority

#43 - sim3C should make use of a observer pattern

Issue - State: open - Opened by cerebis over 8 years ago
Labels: enhancement, low priority

#43 - sim3C should make use of a observer pattern

Issue - State: open - Opened by cerebis over 8 years ago
Labels: enhancement, low priority

#42 - SimForward must gracefully handle templates without cutsites

Issue - State: closed - Opened by cerebis over 8 years ago - 2 comments
Labels: bug, high priority

#42 - SimForward must gracefully handle templates without cutsites

Issue - State: closed - Opened by cerebis over 8 years ago - 2 comments
Labels: bug, high priority

#41 - Simulating sequencing reads

Issue - State: closed - Opened by cerebis over 8 years ago
Labels: enhancement, high priority

#41 - Simulating sequencing reads

Issue - State: closed - Opened by cerebis over 8 years ago
Labels: enhancement, high priority

#40 - BWA MEM mapping can produce no mapped reads to some contigs

Issue - State: open - Opened by cerebis over 8 years ago - 6 comments
Labels: question, Research

#40 - BWA MEM mapping can produce no mapped reads to some contigs

Issue - State: open - Opened by cerebis over 8 years ago - 6 comments
Labels: question, Research

#39 - Ability to simulate simple 3D structure in Hi-C/3C reads

Issue - State: open - Opened by koadman over 8 years ago - 17 comments

#39 - Ability to simulate simple 3D structure in Hi-C/3C reads

Issue - State: open - Opened by koadman over 8 years ago - 17 comments

#38 - Add procedural tree and profile support to workflow

Issue - State: closed - Opened by cerebis over 8 years ago - 1 comment
Labels: enhancement, high priority

#38 - Add procedural tree and profile support to workflow

Issue - State: closed - Opened by cerebis over 8 years ago - 1 comment
Labels: enhancement, high priority

#37 - simForward.py appears to have a minor defect in sample from distributions

Issue - State: closed - Opened by cerebis over 8 years ago - 1 comment
Labels: bug, high priority

#37 - simForward.py appears to have a minor defect in sample from distributions

Issue - State: closed - Opened by cerebis over 8 years ago - 1 comment
Labels: bug, high priority

#36 - Assigning profiles within and across trees.

Issue - State: closed - Opened by cerebis over 8 years ago - 3 comments
Labels: enhancement, low priority

#36 - Assigning profiles within and across trees.

Issue - State: closed - Opened by cerebis over 8 years ago - 3 comments
Labels: enhancement, low priority

#35 - Procedural abundance profiles

Issue - State: closed - Opened by cerebis over 8 years ago - 2 comments

#35 - Procedural abundance profiles

Issue - State: closed - Opened by cerebis over 8 years ago - 2 comments

#34 - Non-deterministic cache misses

Issue - State: closed - Opened by cerebis over 8 years ago - 4 comments

#34 - Non-deterministic cache misses

Issue - State: closed - Opened by cerebis over 8 years ago - 4 comments

#33 - Cached custom objects rely on weak hash codes

Issue - State: closed - Opened by cerebis over 8 years ago - 6 comments
Labels: bug, wontfix

#33 - Cached custom objects rely on weak hash codes

Issue - State: closed - Opened by cerebis over 8 years ago - 6 comments
Labels: bug, wontfix

#32 - Nextflow resume is broken by the NamedValue helper class

Issue - State: closed - Opened by cerebis over 8 years ago - 1 comment
Labels: bug, high priority

#32 - Nextflow resume is broken by the NamedValue helper class

Issue - State: closed - Opened by cerebis over 8 years ago - 1 comment
Labels: bug, high priority

#31 - phylogenetic tree generation

Issue - State: closed - Opened by cerebis over 8 years ago - 8 comments
Labels: enhancement

#31 - phylogenetic tree generation

Issue - State: closed - Opened by cerebis over 8 years ago - 8 comments
Labels: enhancement

#30 - support a 'local' config outside the repo

Issue - State: closed - Opened by koadman over 8 years ago
Labels: enhancement, low priority

#30 - support a 'local' config outside the repo

Issue - State: closed - Opened by koadman over 8 years ago
Labels: enhancement, low priority