bcgsc/orca issues and pull requests

#105 - Cleaning up top-level Dockerfile

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

#104 - Update versions.tsv and index.md

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

#103 - Skip "brew test squeakr" for new build

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

#102 - Build fix: changing reinstall method in Dockerfile

Pull Request - State: closed - Opened by dmohadjel over 5 years ago - 4 comments

#101 - New build fixes, upgrades, uninstalls

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

#100 - Addressing new failed tests

Issue - State: closed - Opened by dmohadjel over 5 years ago - 13 comments
Labels: bug

#99 - Updated files for ORCA

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

#98 - Clean-up of files following 2019.05.16

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

#97 - Build fixes, upgrades

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

#96 - Addressing Docker build failed tests

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

#95 - Problems in including new bottles

Issue - State: closed - Opened by stefcamp over 5 years ago - 1 comment
Labels: question

#94 - Address failed tests

Issue - State: closed - Opened by sjackman over 5 years ago - 29 comments
Labels: bug

#93 - Fix to temporary apt-get install of man-db

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

#92 - Bugfix to upgrading quicktree

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

#91 - Temporarily add `brew update quicktree`

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

#90 - Fixes for orca-6 Docker build

Pull Request - State: closed - Opened by lcoombe almost 6 years ago - 4 comments

#89 - Add temporary 'brew update' to orca-6 Dockerfile

Pull Request - State: closed - Opened by lcoombe almost 6 years ago

#88 - Revert "Use fully-qualified name for wiggletools"

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

#87 - Remove readseq from ORCA

Pull Request - State: closed - Opened by lcoombe almost 6 years ago - 2 comments

#86 - Use fully-qualified name for wiggletools

Pull Request - State: closed - Opened by lcoombe almost 6 years ago - 4 comments

#85 - Temporarily add 'brew upgrade ntcard'

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

#84 - Remove phylip

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

#83 - Temporarily remove pymol from ORCA

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

#82 - man-db: Change installation to 'apt-get install'

Pull Request - State: closed - Opened by lcoombe almost 6 years ago

#81 - Remove 'share/man/ja' directory

Pull Request - State: closed - Opened by lcoombe almost 6 years ago - 2 comments

#80 - Temporarily remove abricate, uninstall jdk

Pull Request - State: closed - Opened by lcoombe almost 6 years ago - 2 comments

#79 - Temporarily remove bandage

Pull Request - State: closed - Opened by lcoombe almost 6 years ago - 2 comments

#78 - Add 34 tools to ORCA

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

#77 - Add temporary `brew update` to orca-2/Dockerfile

Pull Request - State: closed - Opened by lcoombe almost 6 years ago

#76 - Adding tools: ntedit,nthits,rails

Pull Request - State: closed - Opened by lcoombe almost 6 years ago
Labels: enhancement

#75 - Remove mysql - due to build error

Pull Request - State: closed - Opened by lcoombe almost 6 years ago

#74 - Update version of linuxbrew to 2.0.5

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

#73 - Singularity full build

Pull Request - State: closed - Opened by suujia over 6 years ago - 1 comment
Labels: enhancement

#72 - Update tools for new docker build

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

#71 - Singularity basic build

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

#70 - Ignore tools that fail linkage test

Pull Request - State: closed - Opened by suujia over 6 years ago - 2 comments
Labels: bug

#69 - Remove anvio, bam2wig, exabayes

Pull Request - State: closed - Opened by suujia over 6 years ago - 1 comment
Labels: bug

#68 - Add abricate and bandage

Pull Request - State: closed - Opened by suujia over 6 years ago - 1 comment
Labels: enhancement

#67 - Remove cerulean: unmaintained tool

Pull Request - State: closed - Opened by suujia over 6 years ago - 3 comments
Labels: bug

#66 - Disable tests for execution expired tools

Pull Request - State: closed - Opened by suujia over 6 years ago - 4 comments

#65 - Login script for orca Singularity user

Pull Request - State: closed - Opened by suujia over 6 years ago - 2 comments
Labels: enhancement

#64 - Pysam: use unstable release for python 3.7

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

#63 - Broken Tools

Issue - State: closed - Opened by suujia over 6 years ago - 24 comments
Labels: bug

#62 - SLURM job scheduler

Issue - State: open - Opened by suujia over 6 years ago - 3 comments

#61 - orca-1: Remove htseq

Pull Request - State: closed - Opened by sjackman over 6 years ago
Labels: bug

#60 - htseq: error: too many arguments to function

Issue - State: open - Opened by sjackman over 6 years ago - 11 comments
Labels: bug

#59 - add 46 tools

Pull Request - State: closed - Opened by suujia over 6 years ago - 1 comment
Labels: enhancement

#58 - Add missing brewsci/bio formulae to ORCA

Issue - State: closed - Opened by sjackman over 6 years ago - 3 comments
Labels: enhancement

#57 - Singularity build

Issue - State: open - Opened by suujia over 6 years ago - 17 comments

#56 - Build dockerfile with Quay

Issue - State: closed - Opened by suujia over 6 years ago - 16 comments

#55 - Initial migrate container file

Pull Request - State: closed - Opened by suujia over 6 years ago - 14 comments
Labels: enhancement

#54 - orca: Install python-igraph for trans-abyss

Pull Request - State: closed - Opened by sjackman over 6 years ago
Labels: bug

#53 - docker.test.yml: Disable the test of nonpareil

Pull Request - State: closed - Opened by sjackman over 6 years ago - 1 comment
Labels: bug

#52 - dockerfile_lint import default rules

Pull Request - State: closed - Opened by suujia over 6 years ago - 4 comments

#51 - dockerfilelint to dockerfile_lint

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

#50 - orca-5: Remove poretools - brewsci/homebrew-bio#266

Pull Request - State: closed - Opened by suujia over 6 years ago - 9 comments

#49 - orca-1: install biopython for python2

Pull Request - State: closed - Opened by suujia almost 7 years ago - 1 comment
Labels: bug

#48 - Failed Tests

Issue - State: closed - Opened by suujia almost 7 years ago - 18 comments
Labels: bug

#47 - Fix failed tests

Issue - State: closed - Opened by sjackman almost 7 years ago - 1 comment
Labels: bug

#46 - orca-1: Change base image to bcgsc/orca-0

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

#45 - orca-3: Install wamerican for icu4c

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

#44 - Singularity:Overview

Issue - State: open - Opened by tmozgach about 7 years ago - 4 comments

#43 - Singularity: appropriate workaround?

Issue - State: open - Opened by tmozgach about 7 years ago - 2 comments

#42 - Documentation that Steve asked (for users)

Pull Request - State: closed - Opened by tmozgach over 7 years ago - 8 comments

#41 - First draft of technical documentation

Pull Request - State: closed - Opened by tmozgach over 7 years ago - 4 comments
Labels: enhancement

#40 - Update orca.hackton

Pull Request - State: closed - Opened by tmozgach over 7 years ago - 2 comments
Labels: enhancement

#39 - Hackseq scripts:

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

#38 - Change bash to bash -l

Issue - State: closed - Opened by sjackman over 7 years ago - 1 comment
Labels: bug

#37 - Correct message: ~/Software/bin

Issue - State: closed - Opened by sjackman over 7 years ago - 1 comment
Labels: bug

#36 - Add hub to the ORCA image

Issue - State: closed - Opened by sjackman over 7 years ago - 1 comment
Labels: enhancement, wontfix

#35 - Add jupyter to the ORCA image

Issue - State: closed - Opened by sjackman over 7 years ago - 3 comments

#34 - Write Documentation

Issue - State: closed - Opened by tmozgach over 7 years ago - 6 comments

#33 - Migrate containers

Issue - State: open - Opened by tmozgach over 7 years ago - 13 comments

#32 - ORCA paper

Issue - State: closed - Opened by tmozgach over 7 years ago - 10 comments

#31 - Singularity: linubrew folder disappers with --writable flag

Issue - State: open - Opened by tmozgach over 7 years ago - 1 comment

#30 - brew install ... doesn't work (Martin's class)

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

#29 - Run GUI apps in a container

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

#28 - Install for HackSeq image

Issue - State: closed - Opened by sjackman over 7 years ago - 3 comments

#27 - brew cite

Issue - State: closed - Opened by sjackman over 7 years ago - 1 comment
Labels: enhancement, wontfix

#26 - Table of GitHub metadata and analytics

Issue - State: open - Opened by sjackman over 7 years ago - 10 comments

#25 - Formulae fail after updating boost, linuxbrew

Issue - State: open - Opened by tmozgach over 7 years ago - 19 comments

#24 - [email protected] fails.

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

#23 - Add unicycler

Issue - State: closed - Opened by sjackman over 7 years ago - 2 comments
Labels: enhancement

#22 - Have to be fixed before 2017.08 release

Issue - State: open - Opened by tmozgach over 7 years ago - 2 comments

#21 - poretools

Issue - State: closed - Opened by tmozgach over 7 years ago - 6 comments

#20 - mira: exp_flexer.cc

Issue - State: open - Opened by tmozgach over 7 years ago - 7 comments

#19 - discovardenovo

Issue - State: open - Opened by tmozgach over 7 years ago - 8 comments

#18 - Packages cannot be bottled cause they have Perl/Python package dependency

Issue - State: open - Opened by tmozgach over 7 years ago - 1 comment

#17 - BioPerl: FAIL Installing Bio::Root::Version failed

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

#15 - Fix brew linkage --test [email protected]

Issue - State: closed - Opened by tmozgach over 7 years ago - 3 comments

#14 - Fix broken brew linkage --test

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

#13 - Determine license

Issue - State: closed - Opened by sjackman over 7 years ago - 4 comments

#10 - Revise README.md

Issue - State: closed - Opened by sjackman over 7 years ago
Labels: enhancement

#9 - Install cwltool

Issue - State: closed - Opened by sjackman over 7 years ago - 2 comments
Labels: enhancement

#8 - Run dockerfilelint using TravisCI

Issue - State: closed - Opened by sjackman over 7 years ago - 2 comments
Labels: enhancement

#7 - For future

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

#6 - Tag a stable release of ORCA

Issue - State: open - Opened by sjackman over 7 years ago - 1 comment
Labels: enhancement

#4 - BioBuilds vs ORCA (Missing software)

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

#3 - Fix broken brew test

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

#2 - Fix broken formulae

Issue - State: open - Opened by tmozgach over 7 years ago - 1 comment

GitHub / bcgsc/orca issues and pull requests