Ecosyste.ms: Issues

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

GitHub / BD2KGenomics/protect issues and pull requests

#293 - Error when using Dockerized PHLAT

Issue - State: open - Opened by rbowenj over 3 years ago

#292 - Updated to python3

Pull Request - State: open - Opened by drkthomp over 3 years ago - 4 comments

#291 - Python3 adaptation

Pull Request - State: open - Opened by drkthomp almost 4 years ago - 1 comment

#290 - numerically sort positions in vcfs

Issue - State: open - Opened by arkal over 6 years ago - 2 comments

#289 - Dont fail if transgene finds zero actionable mutations (resolves #214)

Pull Request - State: open - Opened by davidstew over 6 years ago
Labels: in progress

#288 - Add fusion filters for transgene (resolves #237)

Pull Request - State: open - Opened by arkal over 6 years ago - 2 comments
Labels: in progress

#287 - providing fusion.bedpe is not compatible with snv calling

Issue - State: closed - Opened by arkal over 6 years ago - 1 comment

#286 - Allow user to specify majority

Issue - State: open - Opened by arkal over 6 years ago

#285 - Fix event with inconsistency in normals with many IARS(resolves #284)

Pull Request - State: closed - Opened by arkal over 6 years ago

#284 - Do not fail if >1 IARS and not all have no normal seq

Issue - State: closed - Opened by arkal over 6 years ago

#283 - Add mix and match functionality for mutation calling (resolves #265)

Pull Request - State: open - Opened by davidstew over 6 years ago
Labels: in progress

#282 - Export transgene fusions (resolves #281)

Pull Request - State: closed - Opened by arkal over 6 years ago

#281 - Transgene does not export fusions

Issue - State: closed - Opened by arkal over 6 years ago

#280 - Cherry pick from master

Pull Request - State: closed - Opened by arkal over 6 years ago

#279 - Add memory requirement to DNA alignment (resolves #278)

Pull Request - State: closed - Opened by arkal over 6 years ago

#278 - Add memory requirements for DNA alignment DAG

Issue - State: closed - Opened by arkal over 6 years ago

#277 - Add troubleshooting to MANUAL.md (resolves #274)

Pull Request - State: closed - Opened by arkal over 6 years ago

#276 - Transfer license to UCSC CGL (resolves #272)

Pull Request - State: closed - Opened by arkal over 6 years ago

#275 - Make saving logs (if possible) a univ_option

Issue - State: open - Opened by arkal over 6 years ago

#274 - Add troubleshooting section to the manual

Issue - State: closed - Opened by davidstew over 6 years ago

#273 - Create LICENSE and move old license to the attic (Resolves #271)

Pull Request - State: closed - Opened by arkal over 6 years ago

#272 - Transfer license to UCSC CGL

Issue - State: closed - Opened by arkal over 6 years ago

#271 - Add github compatible license

Issue - State: closed - Opened by arkal over 6 years ago

#270 - Add Github compatible license

Pull Request - State: closed - Opened by arkal over 6 years ago

#269 - Allow choice of pMHC predictors

Issue - State: open - Opened by davidstew over 6 years ago

#268 - test new docker files

Pull Request - State: closed - Opened by davidstew over 6 years ago - 5 comments

#267 - Fix the setuptools code so that the correct names are used (resolves #266)

Pull Request - State: closed - Opened by swp930 over 6 years ago - 2 comments

#266 - Fix setuptools issue

Issue - State: closed - Opened by arkal over 6 years ago

#265 - Allow mix and match of mutation callers

Issue - State: open - Opened by arkal over 6 years ago
Labels: in progress

#264 - Make section in manual on contributions

Issue - State: open - Opened by arkal over 6 years ago

#263 - change the logging messages so that they occur after events (resolves #254)

Pull Request - State: closed - Opened by davidstew over 6 years ago - 1 comment

#262 - Update flowchart to show that indels and fusions are implemented (resolves #258)

Pull Request - State: closed - Opened by swp930 over 6 years ago - 3 comments

#261 - Update make-prepare to install toil 3.8.0 (resolves #260)

Pull Request - State: closed - Opened by davidstew over 6 years ago - 3 comments

#260 - Update toil in make prepare to 3.8.0

Issue - State: closed - Opened by arkal over 6 years ago

#259 - This commit will modify the logging for after-the-event (resolves [ticket # 254])

Pull Request - State: closed - Opened by swp930 over 6 years ago - 3 comments

#258 - Update flowchart

Issue - State: closed - Opened by arkal over 6 years ago

#257 - Add better support for ProTECT-your-way (resolves #256)

Pull Request - State: closed - Opened by arkal over 6 years ago - 1 comment

#256 - Better support for ProTECT-your-way

Issue - State: closed - Opened by arkal over 6 years ago

#255 - Ensure resource requirements are provided for EACH job

Issue - State: open - Opened by arkal over 6 years ago

#254 - modify all logging to be after-the-event

Issue - State: closed - Opened by arkal over 6 years ago

#253 - Better help with Protect --help

Issue - State: open - Opened by arkal over 6 years ago

#252 - Show example

Pull Request - State: closed - Opened by arkal over 6 years ago

#251 - Fix toil in setup.py (resolves #250)

Pull Request - State: closed - Opened by arkal over 6 years ago

#250 - Fix toil in setup.py

Issue - State: closed - Opened by arkal over 6 years ago

#249 - Consider MHCFlurry

Issue - State: open - Opened by arkal over 6 years ago

#248 - Citable reference

Issue - State: open - Opened by schelhorn over 6 years ago - 2 comments

#247 - Consider DeepMHC

Issue - State: open - Opened by arkal over 6 years ago

#246 - Diagnose "Removal In Progress" Errors with MHCI dockers

Issue - State: closed - Opened by arkal over 6 years ago - 1 comment

#245 - Diagnose "Removal In Progress

Issue - State: open - Opened by arkal over 6 years ago

#244 - Provide memory requirement for Fusions

Issue - State: closed - Opened by arkal over 6 years ago - 1 comment

#243 - Allow startup with expression and fusion bedpe (resolves #242)

Pull Request - State: closed - Opened by arkal almost 7 years ago - 2 comments

#242 - allow user to provide fusions and expression

Issue - State: closed - Opened by arkal almost 7 years ago

#241 - Implement indel support (resolves#2)

Pull Request - State: closed - Opened by arkal almost 7 years ago - 6 comments

#240 - get_patient_vcf should return a filestore ID not a file path

Issue - State: closed - Opened by arkal almost 7 years ago - 1 comment

#239 - left align indels

Issue - State: open - Opened by arkal almost 7 years ago - 1 comment

#238 - Upgrade to mhci:2.17

Issue - State: open - Opened by arkal almost 7 years ago

#237 - Disregard mitochondrial and rna-gene fusions

Issue - State: open - Opened by arkal almost 7 years ago
Labels: in progress

#236 - Cherry pick from master (#232, #234)

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

#235 - Update rankboost to 2.1.1 (resolves #234)

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

#234 - Collapse dupes in rankboost

Issue - State: closed - Opened by arkal almost 7 years ago

#233 - Gracefully handle no actionable mutations (resolves #232)

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

#232 - gracefully handle no actionable mutations

Issue - State: closed - Opened by arkal about 7 years ago

#231 - fix the names of output files for rna and mhci and mhcii

Pull Request - State: closed - Opened by wshands about 7 years ago - 1 comment

#230 - Add mark duplicates to DNA processing (resolves #229)

Pull Request - State: closed - Opened by arkal about 7 years ago - 1 comment

#229 - Add best practices modules

Issue - State: closed - Opened by arkal about 7 years ago

#228 - Filename different in S3 vs wrapper.py

Issue - State: closed - Opened by wshands about 7 years ago - 1 comment

#227 - Issues/226 fix cwl options

Pull Request - State: closed - Opened by wshands about 7 years ago

#226 - fix protect.cwl options

Issue - State: closed - Opened by wshands about 7 years ago

#225 - Need tag for release 2.5.1 to support Dockstore

Issue - State: closed - Opened by wshands about 7 years ago - 1 comment

#224 - Dockerfile so that ProTECT versions can be validated in Dockstore (re…

Pull Request - State: closed - Opened by wshands about 7 years ago - 4 comments

#223 - Dockstore requires 'Dockerfile' in repository

Issue - State: closed - Opened by wshands about 7 years ago

#222 - Fix Makefiles to not crash on release jenkins runs

Issue - State: open - Opened by arkal about 7 years ago

#221 - Add cwl fixes (resolves #218)

Pull Request - State: closed - Opened by arkal about 7 years ago

#220 - Update setuptools in venv to fix pypi migration

Issue - State: closed - Opened by arkal about 7 years ago

#219 - Issue/add prefix #218

Pull Request - State: closed - Opened by wshands over 7 years ago - 6 comments

#218 - Add missing --prefix and fix format error in CWL

Issue - State: closed - Opened by wshands over 7 years ago

#216 - Fix annotations.txt in gdc download (resolves #215)

Pull Request - State: closed - Opened by arkal over 7 years ago

#215 - Some gdc samples can have annotations.txt

Issue - State: closed - Opened by arkal over 7 years ago

#214 - Don't fail if transgene finds 0 actionable mutations

Issue - State: open - Opened by arkal over 7 years ago
Labels: in progress

#213 - Blacklist gdc 1.2.0 (resolves #210)

Pull Request - State: closed - Opened by arkal over 7 years ago

#212 - Add code to ensure gdc-client v1.2.0 is blacklisted (resolves #210)

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

#211 - Fix cwl descriptor (resolves #207)

Pull Request - State: closed - Opened by arkal over 7 years ago

#210 - Blacklist gdc-client v1.2.0

Issue - State: closed - Opened by arkal over 7 years ago - 5 comments

#209 - Fix CWL descriptor and dockstore support (resolves #207)

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

#208 - Updated CWL descriptor (resolves #207)

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

#207 - Protect CWL descriptor fixes

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

#206 - Modify dockerfile to safe-remove toil.git always

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

#205 - Fix broken fusion test (resolves #204)

Pull Request - State: closed - Opened by arkal over 7 years ago

#204 - fix broken fusion tests

Issue - State: closed - Opened by arkal over 7 years ago

#203 - Bump toil to 3.8.0 (resolves #202)

Pull Request - State: closed - Opened by arkal over 7 years ago

#202 - Bump Toil to 3.8.0

Issue - State: closed - Opened by arkal over 7 years ago

#201 - Disallow fusion detection without input Tumor RNA fastq (resolves #197)

Pull Request - State: closed - Opened by arkal over 7 years ago

#125 - Fix --limitBAMsortRAM in STAR

Issue - State: closed - Opened by arkal almost 8 years ago - 1 comment

#92 - Add fusion support (resolves #1)

Pull Request - State: closed - Opened by jpfeil about 8 years ago - 19 comments

#34 - Add vardict support

Issue - State: open - Opened by arkal over 8 years ago - 9 comments

#21 - Use BWA to add read groups

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

#2 - Implement Indel support

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

#1 - Implement Fusion support

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