standage/genhub issues and pull requests

#95 - Latest RefSeq recipe for Hymenoptera references

Pull Request - State: closed - Opened by standage over 5 years ago

#94 - Add support for obsolete RefSeq reference genomes

Pull Request - State: closed - Opened by standage over 5 years ago - 3 comments

#93 - using yaml.safe_load as per https://github.com/yaml/pyyaml/wiki/PyYAM…

Pull Request - State: closed - Opened by vpbrendel over 5 years ago - 1 comment

#92 - Updated name to reflect new name on NCBI

Pull Request - State: closed - Opened by timlai4 over 5 years ago - 2 comments

#91 - Update broken config for Aedes aegypti

Pull Request - State: closed - Opened by standage almost 7 years ago

#90 - Restoring support for HymenopteraBase reference genomes

Pull Request - State: closed - Opened by standage over 7 years ago - 2 comments

#89 - Update configs for reference genomes

Pull Request - State: closed - Opened by standage over 7 years ago - 1 comment

#88 - Update configs

Pull Request - State: closed - Opened by standage over 7 years ago - 1 comment

#87 - Add support for GenBank sequences, add Znev as a reference genome

Pull Request - State: closed - Opened by standage over 7 years ago - 1 comment

#86 - Banana genome

Pull Request - State: closed - Opened by standage over 8 years ago - 1 comment

#85 - New script for maintaining a cache of RefSeq genomes

Pull Request - State: closed - Opened by standage over 8 years ago

#84 - Download exception handling

Pull Request - State: closed - Opened by standage over 8 years ago - 1 comment

#83 - Data validation updates

Pull Request - State: closed - Opened by standage over 8 years ago - 1 comment

#82 - New protein->iLocus mapping file

Pull Request - State: closed - Opened by standage over 8 years ago - 1 comment

#81 - Easily identify piLocus representatives

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

#80 - Create spec file for GFF3 input, integrate into workflow

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

#79 - Painless transition from nose to py.test. Closes #73.

Pull Request - State: closed - Opened by standage over 8 years ago

#78 - New Amel annotation

Pull Request - State: closed - Opened by standage over 8 years ago - 1 comment

#77 - Updates to documentation and ancillary files

Pull Request - State: closed - Opened by standage over 8 years ago - 2 comments

#76 - Checksums missing for G. raimondii config

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

#75 - New Amel genome

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

#74 - Option for overriding integrity (shasum) check

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

#73 - nose --> py.test

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

#72 - Add documentation for creating new .yml config files

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

#71 - .txt --> .tsv for some ancillary data files

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

#70 - LocusPocus Fidibus!

Pull Request - State: closed - Opened by standage almost 9 years ago

#69 - Deprecate `*.simple-iloci.txt` file

Issue - State: open - Opened by standage almost 9 years ago - 1 comment

#68 - Another mosquito genome

Pull Request - State: closed - Opened by standage almost 9 years ago - 1 comment

#67 - piLocus type for pre-mRNA, mRNA, exon, and intron TSV files

Issue - State: open - Opened by standage almost 9 years ago

#66 - Support for generic input

Issue - State: closed - Opened by standage almost 9 years ago - 1 comment

#65 - Spider mite genome

Pull Request - State: closed - Opened by standage almost 9 years ago - 1 comment

#64 - Shuffled data and non memory limits for `cluster` task

Pull Request - State: closed - Opened by standage almost 9 years ago

#63 - Script for calculating phi/sigma measures of genome compactness

Pull Request - State: closed - Opened by standage almost 9 years ago - 2 comments

#62 - New recipes

Pull Request - State: closed - Opened by standage almost 9 years ago - 1 comment

#61 - RefSeq annotations for Pdom, Pcan, Dqua

Pull Request - State: closed - Opened by standage almost 9 years ago - 1 comment

#60 - Configuration registry is cumbersome

Issue - State: closed - Opened by standage almost 9 years ago

#59 - Docs cleanup

Pull Request - State: closed - Opened by standage almost 9 years ago

#58 - New recipe for Daphnia

Pull Request - State: closed - Opened by standage almost 9 years ago - 1 comment

#57 - Script to compute iLocus summary

Pull Request - State: closed - Opened by standage almost 9 years ago

#56 - Correct iLocus type reporting

Pull Request - State: closed - Opened by standage almost 9 years ago

#55 - New `--cdargs` option.

Pull Request - State: closed - Opened by standage almost 9 years ago - 1 comment

#54 - New rice recipe

Pull Request - State: closed - Opened by standage almost 9 years ago - 1 comment

#53 - Add new `seqfilter` mechanism

Pull Request - State: closed - Opened by standage almost 9 years ago - 1 comment

#52 - NT_ and NW_ accessions in mammalian genomes correspond to patches, variants

Issue - State: closed - Opened by standage almost 9 years ago

#51 - Allow user to override cd-hit defaults

Issue - State: closed - Opened by standage almost 9 years ago

#50 - Closes #48.

Pull Request - State: closed - Opened by standage almost 9 years ago - 1 comment

#49 - New rice recipe?

Issue - State: closed - Opened by standage almost 9 years ago

#48 - Add `delta` option to genhub-build script

Issue - State: closed - Opened by standage almost 9 years ago

#47 - Overlapping exons prematurely kill C. reinhardtii build

Issue - State: open - Opened by standage almost 9 years ago

#46 - iLocus label formatting, table cleanup

Pull Request - State: closed - Opened by standage almost 9 years ago

#45 - Cluster task for hiLoci

Pull Request - State: closed - Opened by standage almost 9 years ago - 1 comment

#44 - Implement cleanup task

Pull Request - State: closed - Opened by standage almost 9 years ago - 1 comment

#43 - Green algae recipes

Pull Request - State: closed - Opened by standage about 9 years ago - 1 comment

#42 - Integrate TAIR and Amel OGS recipes

Pull Request - State: closed - Opened by standage about 9 years ago

#41 - Recipes for green algae

Issue - State: closed - Opened by standage about 9 years ago

#40 - Better handling of multiprocessing pool

Issue - State: closed - Opened by standage about 9 years ago

#39 - Recipes for specific versions

Issue - State: closed - Opened by standage about 9 years ago - 2 comments

#38 - Three new genome recipes

Pull Request - State: closed - Opened by standage about 9 years ago - 1 comment

#37 - Fix typos in developer docs; trigger badge refresh (hopefully)

Pull Request - State: closed - Opened by standage about 9 years ago

#36 - Extend RefSeq module with support for GenBank

Issue - State: closed - Opened by standage about 9 years ago

#35 - Test whether ilens file can be ignored

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

#34 - Move Dmel to updated RefSeq GenomeDB config.

Pull Request - State: closed - Opened by standage about 9 years ago

#33 - Multiprocessing support!

Pull Request - State: closed - Opened by standage about 9 years ago

#32 - Replace `conf` module with `registry` module

Pull Request - State: closed - Opened by standage about 9 years ago

#31 - Add rice and medicago genomes

Pull Request - State: closed - Opened by standage about 9 years ago

#30 - More PycURL stuff

Issue - State: closed - Opened by standage about 9 years ago

#29 - Move, rename config files

Issue - State: closed - Opened by standage about 9 years ago

#28 - Polish documentation, dev environment

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

#27 - Merge 'stats' branch

Pull Request - State: closed - Opened by standage about 9 years ago

#26 - Fix mRNA parsing bug

Pull Request - State: closed - Opened by standage about 9 years ago

#25 - Merge 'datatypes' branch

Pull Request - State: closed - Opened by standage about 9 years ago

#24 - Merge 'modorg' branch

Pull Request - State: closed - Opened by standage about 9 years ago

#23 - New RefSeq module

Pull Request - State: closed - Opened by standage about 9 years ago

#22 - Improved `format` script

Pull Request - State: closed - Opened by standage about 9 years ago

#21 - Merge refactor branch

Pull Request - State: closed - Opened by standage about 9 years ago

#20 - Merge CRG branch

Pull Request - State: closed - Opened by standage about 9 years ago

#19 - Switch over to newer NCBI genomes FTP

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

#18 - Merge BeeBase branch

Pull Request - State: closed - Opened by standage over 9 years ago - 1 comment

#17 - Refactor `format.py`

Issue - State: closed - Opened by standage over 9 years ago

#16 - Pass source to `genhub-format-gff3.py`

Issue - State: closed - Opened by standage over 9 years ago

#15 - Improve configuration parsing

Issue - State: closed - Opened by standage over 9 years ago - 3 comments

#14 - Dmel downloading and formatting now handled correctly

Pull Request - State: closed - Opened by standage over 9 years ago

#13 - Dmel format task fails

Issue - State: closed - Opened by standage over 9 years ago

#12 - CodeClimate config

Pull Request - State: closed - Opened by standage over 9 years ago

#11 - No which output

Pull Request - State: closed - Opened by standage over 9 years ago

#10 - CodeClimate integration

Pull Request - State: closed - Opened by standage over 9 years ago

#9 - Polishing up Pdom configuration and testing

Pull Request - State: closed - Opened by standage over 9 years ago

#8 - Closes #6.

Pull Request - State: closed - Opened by standage over 9 years ago

#7 - More species to integrate

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

#6 - Support for lists of conf files

Issue - State: closed - Opened by standage over 9 years ago

#5 - Cache dependencies

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

#4 - Script names

Issue - State: closed - Opened by standage over 9 years ago

#3 - Script paths during build

Issue - State: closed - Opened by standage over 9 years ago

#2 - Consolidate file name resolution

Issue - State: closed - Opened by standage over 9 years ago

#1 - Update `check.py` to check for PATH dependencies

Issue - State: closed - Opened by standage over 9 years ago

GitHub / standage/genhub issues and pull requests