orca

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Singularity: linubrew folder disappers with --writable flag

1

**Problem:** usually a singularity container is read-only (brew install, apt-get don't work). In order to edit a container, --writable flag is used. However, the `brew` command disappeared (see a sample...

tmozgach

Tag a stable release of ORCA

1

+ [x] Create an automated build for `bcgsc/orca` using https://hub.docker.com + [x] Create an automated test using Docker Compose to run `brew test` for each installed formula and also `brew...

sjackman

mira: exp_flexer.cc

7

``` ==> Installing homebrew/science/mira ==> Downloading https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira-4.0.2.tar.bz2 ==> Downloading from https://superb-dca2.dl.sourceforge.net/project/mira-assembler/MIRA/stable/mira-4.0.2.tar.bz2 ######################################################################## 100.0% ==> ./configure --prefix=/home/linuxbrew/.linuxbrew/Cellar/mira/4.0.2 --with-expat=/home/linuxbrew/.linuxbrew/opt/expat --with-expat-lib=-L/home/linuxbrew/.linuxbrew/opt/exp ==> make LIBS='-lboost_regex-mt -lboost_system-mt -lboost_filesystem-mt -lboost_iostreams-mt -lboost_thread-mt -lexpat -lz' Last 15 lines...

tmozgach

discovardenovo

8

``` ==> Installing homebrew/science/discovardenovo ==> Downloading ftp://ftp.broadinstitute.org/pub/crd/DiscovarDeNovo/latest_source_code/discovardenovo-52488.tar.gz ######################################################################## 100.0% ==> ./configure --disable-silent-rules --prefix=/home/linuxbrew/.linuxbrew/Cellar/discovardenovo/52488 ==> make install Last 15 lines from /home/linuxbrew/.cache/Homebrew/Logs/discovardenovo/02.make: make[1]: *** [CrossOut] Error 1 make[1]: *** Waiting for...

tmozgach

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

1

- [x] amos https://github.com/Homebrew/homebrew-science/pull/6135 - [ ] graphlan - [ ] maker - [ ] mlst - [ ] prokka - [ ] velvetoptimiser

tmozgach

- [x] biointerchange get rid off it - [x] jdk skip - [x] parsnp - [x] prokka - [ ] blasr https://github.com/bcgsc/orca/issues/3 - [x] fwdpp https://github.com/bcgsc/orca/issues/3 - [ ] lobstr...

tmozgach

Have to be fixed before 2017.08 release

2

`brew install` fails: (The list is based on the high priority list) - [x] delly (https://github.com/Homebrew/homebrew-science/pull/5412) - [ ] discovardenovo (https://github.com/bcgsc/orca/issues/19) - [ ] gubbins (Homebrew/homebrew-science#5752) - [ ] masurca...

tmozgach

Fix broken formulae

1

**The Bold forlmulae** is a forlmulae that exists in the old ORCA and absents in the new ORCA (brew list) - [x] **cufflinks** - [ ] **libdivsufsort** - [ ]...

tmozgach

- [x] apache-spark https://github.com/Homebrew/homebrew-core/pull/14570 - [x] bamm bamm: Enable multithreading to use std::thread: Operation not permitted #5 - [ ] blasr blasr: revision for hdf5 https://github.com/Homebrew/homebrew-science/pull/5688 - [x] biopieces (export...

tmozgach

Create a formula for singularity

1

Please create a formula for Singularity and submit it to https://github.com/Linuxbrew/homebrew-extra http://singularity.lbl.gov/quickstart ```sh brew create --tap=linuxbrew/extra https://github.com/singularityware/singularity/releases/download/2.3.1/singularity-2.3.1.tar.gz ```

sjackman