orca

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Table of GitHub metadata and analytics

10

Hi, Tanya. Can you please prepare a table that lists… + [x] the number of GitHub watchers, stars, and forks for each formula in Homebrew/science that has a GitHub a...

sjackman

Singularity build

17

[shub:bcgsc/orca](https://www.singularity-hub.org/containers/1167/log) [shub:suujia/orca](https://www.singularity-hub.org/containers/3402/log) Not sure how to trigger a rebuild for the bcgsc/orca shub. The error message I got with a build on suujia/orca shub was: ``` + su -c brew...

suujia

SLURM job scheduler

3

The most commonly used job scheduler with Singularity or bioinformatics analysis jobs is Slurm. Here are its benefits: - load balancing between multiple nodes - limiting ram/process job size -...

suujia

htseq: error: too many arguments to function

11

``` pysam/libchtslib.c: In function '__Pyx_PyCFunction_FastCall': pysam/libchtslib.c:15077:12: error: too many arguments to function '(PyObject * (*)(PyObject *, PyObject * const*, Py_ssize_t))meth' return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL); ``` https://hub.docker.com/r/bcgsc/orca-1/builds/brdtjmj5vdtd9ifucknylnu/ @suujia Can...

sjackman

Migrate containers

13

**Problem:** how to migrate a running container from one worker to another worker. **Flocker:?** https://github.com/ClusterHQ/flocker

tmozgach

Singularity:Overview

4

For Singularity version: `2.4.1` Singularity Recipe: https://github.com/bcgsc/orca/blob/master/Singularity.1 Build the image MANUALLY: ``` sudo singularity build orca.simg Singularity1 ``` Each user should create an overlay: ``` singularity image.create --size 3000 overlay.simg...

tmozgach

Singularity: appropriate workaround?

2

@sjackman could you please look into my solution to that problem and tell me, could we do that? Or may be you have a more elegant suggestion. **Given**: an immutable...

tmozgach

Formulae fail after updating boost, linuxbrew

19

Install: - [x] sga works in empty image =>something influences on it Test: - [ ] circlator https://github.com/Homebrew/homebrew-science/pull/6216 - [x] discovar https://github.com/Homebrew/homebrew-science/pull/6275 => RUN brew install [email protected] solves - [x]...

tmozgach

**Temporary solution:** First create this directory: ``` mkdir -p -m775 ~/.cache/Homebrew ``` Then create a .bashrc (dot bashrc) file in their home directory. To do this, you can copy the...

tmozgach

- [ ] biopieces (export variables automatically, example, vcftools {xxx: ,yyy:}) - [ ] zip (create formulae) - [ ] CWL - [ ] a container: delete or exit function

tmozgach