Ecosyste.ms: Issues

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

GitHub / OLC-Bioinformatics/OLCTools issues and pull requests

#67 - ImportError: cannot import name 'kmc' from 'biotools'

Issue - State: open - Opened by joybio over 1 year ago

#66 - AssertionError: "Authorize third-party client" in browser.title

Issue - State: open - Opened by pcrxn almost 2 years ago
Labels: enhancement

#65 - Selenium Authorization Automation

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

#64 - Bam parsing overhaul

Pull Request - State: closed - Opened by lowandrew almost 6 years ago - 1 comment

#62 - Changed header

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

#60 - Fixes

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

#59 - Updates to CLARK, compress.py

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

#58 - Creating proper number of threads now

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

#57 - Forgot to add skesa script

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

#56 - Fixes to reports - issues with MLST formatting.

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

#55 - Updates to MLST and ResFinder reporting

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

#54 - Changes to GDCS reporting

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

#50 - Necessary fixes required for reformatting damaged FASTQ files

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

#49 - Multiple fixes to attempt to deal with non-standard FASTQ reads

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

#48 - Added functionality to copy reports created by confindr and Plasmid_E…

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

#47 - Fixed issue with GenomeQAML not creating path to store reports

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

#46 - Needed to ensure that variable was treated as an integer

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

#45 - Update report to reflect change in plasmid outputs

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

#44 - Incorporated Plasmid_Extractor and GenomeQAML into pipeline

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

#43 - Merge

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

#42 - Added GDCS functionality

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

#41 - Addressed changes in virulence gene database ':' in gene names replac…

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

#40 - ResFinder rules update

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

#39 - Fixes to reporter to report results from all strain; spadesRun now ha…

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

#38 - Updates to geneseekr databasing scheme, import statements, and paths

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

#37 - Fixed import statement to allow pytest to import confindr

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

#36 - Removed more references to quast in spadespipeline/versions.py

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

#35 - Merge

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

#34 - Fixed issue where BAM index file was older than the data file by inc…

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

#33 - Merge

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

#32 - MERGE!

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

#31 - Should be good now.

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

#30 - Fixed issue with non-standard nomenclature in notes.txt file of resfi…

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

#29 - Merge all the things!

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

#28 - Fixed issue with extension for automateCLARK

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

#27 - Changed logic for determining internal clipping - allow a 10 bp windo…

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

#26 - Mostly getting biotools to work with conda version of bbmap

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

#25 - Added keyword argument to baiting method to allow for kmer length sel…

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

#24 - Changed bbmap methods to use self.cpus instead of self.threads

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

#23 - Merge all the things.

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

#22 - Adding optional print to logfile functionality for printtime method

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

#21 - Added keyword argument for average depth. Default is 10

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

#20 - Added sample-specific logfiles to fastq creation script

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

#19 - Added colours!

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

#18 - Maybe this will work this time?

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

#17 - ?

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

#16 - Issues with binaries again!?

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

#15 - Removed __pycache__ from repository

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

#14 - Merge pull request #13 from lowandrew/revert-12-master

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

#13 - Revert "Using bbduk instead of mirabait for read baiting"

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

#12 - Using bbduk instead of mirabait for read baiting

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

#11 - Minor fixes

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

#10 - Added average depth cutoff functionality

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

#8 - Managed to get Escherichia core genomes working. Cleaned up a bit, too

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

#7 - Addressed issue with lack of bestassembly file

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

#6 - Renamed metagenomeFilter to metagenomefilter to avoid conflicts

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

#5 - Fixed issue with sipprcommon no longer being a submodule

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

#4 - More fixes to import statements

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

#3 - Modifications to sipprcommon to fix issues with import statements

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

#2 - Added sipprCommon package

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