Ecosyste.ms: Issues

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

GitHub / karel-brinda/mof-search issues and pull requests

#255 - Add shields to readme

Pull Request - State: closed - Opened by karel-brinda about 1 year ago

#254 - Make download.sh robust and testable

Pull Request - State: closed - Opened by karel-brinda about 1 year ago

#252 - Improve `make help` interface and output

Pull Request - State: closed - Opened by karel-brinda about 1 year ago

#251 - Update colors of comments

Pull Request - State: closed - Opened by karel-brinda about 1 year ago

#250 - fix: filter out empty lines when getting the batches

Pull Request - State: closed - Opened by leoisl about 1 year ago

#249 - Fix "ANSI colors in Make Help command are not being interpreted"

Pull Request - State: closed - Opened by Francii-B about 1 year ago - 4 comments

#248 - ANSI colors in Make Help command are not being interpreted

Issue - State: closed - Opened by Francii-B about 1 year ago - 4 comments
Labels: bug

#247 - Fix/236 (fix Zenodo blocking downloads)

Pull Request - State: closed - Opened by leoisl about 1 year ago - 4 comments

#246 - Decompressing COBS indexes takes way too much RAM

Issue - State: closed - Opened by leoisl about 1 year ago - 1 comment
Labels: IDEAS-FOR-THE-FUTURE

#246 - Decompressing COBS indexes takes way too much RAM

Issue - State: closed - Opened by leoisl about 1 year ago - 1 comment
Labels: IDEAS-FOR-THE-FUTURE

#245 - Add `make download_asms` and `make download_cobs`

Pull Request - State: closed - Opened by Francii-B about 1 year ago

#245 - Add `make download_asms` and `make download_cobs`

Pull Request - State: closed - Opened by Francii-B about 1 year ago

#244 - Add separate subcommands for downloading assemblies and cobs indexes

Issue - State: closed - Opened by Francii-B about 1 year ago
Labels: enhancement

#243 - Task1

Pull Request - State: closed - Opened by Francii-B about 1 year ago

#243 - Task1

Pull Request - State: closed - Opened by Francii-B about 1 year ago

#242 - Number of download threads reportedly being 1 on some machines regardless of the configuration

Issue - State: closed - Opened by karel-brinda about 1 year ago - 12 comments
Labels: bug

#241 - Update documentation

Pull Request - State: closed - Opened by karel-brinda about 1 year ago

#240 - Sometimes snakefmt breaks syntax for lambda functions

Issue - State: closed - Opened by karel-brinda about 1 year ago
Labels: bug

#240 - Sometimes snakefmt breaks syntax for lambda functions

Issue - State: closed - Opened by karel-brinda about 1 year ago
Labels: bug

#239 - Update directory structure & fix readme accordingly

Pull Request - State: closed - Opened by karel-brinda about 1 year ago

#239 - Update directory structure & fix readme accordingly

Pull Request - State: closed - Opened by karel-brinda about 1 year ago

#238 - Update documentation

Pull Request - State: closed - Opened by karel-brinda about 1 year ago

#238 - Update documentation

Pull Request - State: closed - Opened by karel-brinda about 1 year ago

#236 - Zenodo is blocking some downloads

Issue - State: closed - Opened by leoisl about 1 year ago - 20 comments

#235 - fix: fix download issues and re-enables CI on ubuntu and mac and several python versions

Pull Request - State: closed - Opened by leoisl about 1 year ago - 1 comment

#234 - Downloading is not working and `make test` fails

Issue - State: closed - Opened by leoisl about 1 year ago - 6 comments

#234 - Downloading is not working and `make test` fails

Issue - State: closed - Opened by leoisl about 1 year ago - 6 comments

#233 - Add channels to conda command

Pull Request - State: closed - Opened by karel-brinda about 1 year ago

#232 - Update documentation

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#231 - Add a possibility to plug another mapper

Issue - State: open - Opened by karel-brinda over 1 year ago
Labels: enhancement

#231 - Add a possibility to plug another mapper

Issue - State: open - Opened by karel-brinda over 1 year ago
Labels: enhancement

#230 - Fix a typo

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#230 - Fix a typo

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#229 - Update readme

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#229 - Update readme

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#228 - Update readme

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#228 - Update readme

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#227 - Fix max_download_threads in cluster mode

Issue - State: closed - Opened by leoisl over 1 year ago - 2 comments
Labels: duplicate

#226 - Adds functionality to run MOF search in a LSF cluster

Pull Request - State: closed - Opened by leoisl over 1 year ago - 1 comment

#226 - Adds functionality to run MOF search in a LSF cluster

Pull Request - State: closed - Opened by leoisl over 1 year ago - 1 comment

#225 - batch_align.py loads up the whole query fasta into RAM

Issue - State: open - Opened by leoisl almost 2 years ago - 2 comments

#223 - Minimap instances created even for 0 queries (COBS filtering not taken into account for mm2 instance building)

Issue - State: closed - Opened by karel-brinda almost 2 years ago - 2 comments
Labels: bug, high-priority

#221 - End of year and my updates

Issue - State: closed - Opened by leoisl about 2 years ago

#221 - End of year and my updates

Issue - State: closed - Opened by leoisl about 2 years ago

#220 - Measuring pipeline's RAM usage with another method

Pull Request - State: closed - Opened by leoisl about 2 years ago - 26 comments

#219 - Verifying memory consumption measurements

Issue - State: closed - Opened by karel-brinda about 2 years ago - 8 comments
Labels: high-priority, paper

#219 - Verifying memory consumption measurements

Issue - State: closed - Opened by karel-brinda about 2 years ago - 8 comments
Labels: high-priority, paper

#218 - Improve result compression so that it doesn't bias stats

Pull Request - State: closed - Opened by karel-brinda about 2 years ago - 1 comment

#217 - Unified data parameters table

Pull Request - State: closed - Opened by leoisl about 2 years ago - 1 comment

#216 - Optimize result compression for time

Issue - State: closed - Opened by karel-brinda about 2 years ago - 2 comments
Labels: enhancement

#215 - Implementing auto(N) for cobs_threads parameter

Pull Request - State: closed - Opened by leoisl about 2 years ago - 10 comments

#215 - Implementing auto(N) for cobs_threads parameter

Pull Request - State: closed - Opened by leoisl about 2 years ago - 10 comments

#214 - Implement auto(N) for cobs_threads parameter

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

#214 - Implement auto(N) for cobs_threads parameter

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

#213 - Read names in tests are confusing and make debugging difficult

Issue - State: closed - Opened by karel-brinda about 2 years ago - 1 comment

#213 - Read names in tests are confusing and make debugging difficult

Issue - State: closed - Opened by karel-brinda about 2 years ago - 1 comment

#212 - Reformat

Pull Request - State: closed - Opened by karel-brinda about 2 years ago

#211 - Unified data parameters table

Issue - State: closed - Opened by karel-brinda about 2 years ago - 5 comments

#210 - Adding the auto mode; fix 202 and 206

Pull Request - State: closed - Opened by leoisl about 2 years ago - 4 comments

#210 - Adding the auto mode; fix 202 and 206

Pull Request - State: closed - Opened by leoisl about 2 years ago - 4 comments

#208 - Even with mem-stream the IO bottleneck seems to be partially present on OS X

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

#207 - COBS decompression dir disappeared from `config.yaml`

Issue - State: closed - Opened by karel-brinda about 2 years ago - 5 comments
Labels: low-priority

#206 - Number of COBS threads must be proportional to the RAM usage

Issue - State: closed - Opened by leoisl over 2 years ago - 1 comment

#206 - Number of COBS threads must be proportional to the RAM usage

Issue - State: closed - Opened by leoisl over 2 years ago - 1 comment

#205 - Loading cobs directly from memory and implement index_load_mode parameter

Pull Request - State: closed - Opened by leoisl over 2 years ago - 4 comments

#205 - Loading cobs directly from memory and implement index_load_mode parameter

Pull Request - State: closed - Opened by leoisl over 2 years ago - 4 comments

#204 - Implement index_load_mode parameter

Issue - State: closed - Opened by leoisl over 2 years ago

#204 - Implement index_load_mode parameter

Issue - State: closed - Opened by leoisl over 2 years ago

#203 - Indexes are too large and thus are slowing down the pipeline significantly

Issue - State: closed - Opened by leoisl over 2 years ago - 3 comments
Labels: IDEAS-FOR-THE-FUTURE

#202 - Take into account xz decompression (`xzcat`) RAM usage when streaming

Issue - State: closed - Opened by leoisl over 2 years ago - 11 comments

#202 - Take into account xz decompression (`xzcat`) RAM usage when streaming

Issue - State: closed - Opened by leoisl over 2 years ago - 11 comments

#201 - Improve scripts/aggregate_sams.sh

Issue - State: closed - Opened by leoisl over 2 years ago

#201 - Improve scripts/aggregate_sams.sh

Issue - State: closed - Opened by leoisl over 2 years ago

#200 - Exit 0 even if grep does not match anything

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

#200 - Exit 0 even if grep does not match anything

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

#199 - Query results are being cut short

Issue - State: closed - Opened by leoisl over 2 years ago

#199 - Query results are being cut short

Issue - State: closed - Opened by leoisl over 2 years ago

#198 - Trailing empty lines in the batches text file makes the pipeline fail

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

#197 - Load xzed file directly to COBS

Issue - State: closed - Opened by leoisl over 2 years ago - 1 comment

#197 - Load xzed file directly to COBS

Issue - State: closed - Opened by leoisl over 2 years ago - 1 comment

#196 - Add LQ genomes to the dataset

Issue - State: closed - Opened by leoisl over 2 years ago - 5 comments

#196 - Add LQ genomes to the dataset

Issue - State: closed - Opened by leoisl over 2 years ago - 5 comments

#195 - Consider PAF as a possible output format

Issue - State: closed - Opened by karel-brinda over 2 years ago - 1 comment
Labels: IDEAS-FOR-THE-FUTURE

#195 - Consider PAF as a possible output format

Issue - State: closed - Opened by karel-brinda over 2 years ago - 1 comment
Labels: IDEAS-FOR-THE-FUTURE

#194 - Quick rejection of entire batches

Issue - State: closed - Opened by leoisl over 2 years ago - 5 comments
Labels: IDEAS-FOR-THE-FUTURE

#193 - Not storing SAM headers in the minimap output

Pull Request - State: closed - Opened by leoisl over 2 years ago

#193 - Not storing SAM headers in the minimap output

Pull Request - State: closed - Opened by leoisl over 2 years ago

#192 - gzcat -> gunzip --stdout

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

#192 - gzcat -> gunzip --stdout

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

#191 - Nothing is mapped on main branch

Issue - State: closed - Opened by leoisl over 2 years ago - 1 comment
Labels: bug

#191 - Nothing is mapped on main branch

Issue - State: closed - Opened by leoisl over 2 years ago - 1 comment
Labels: bug

#190 - Mapping despite no candidates (probably)

Issue - State: closed - Opened by karel-brinda over 2 years ago - 3 comments
Labels: bug