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@michaelbarton
michaelbarton / spades_log.txt
Created Sep 15, 2017
Spades log on unnormalised single cell data
View spades_log.txt
+ TASK=merge
++ fetch_task_from_taskfile.sh /usr/local/share/Taskfile merge
+ CMD=' production_pipeline_merged_reads.sh ${READS} ${CONTIGS}'
++ biobox_args.sh 'select(has("fastq")) | .fastq | map(.value) | join(",")'
+ READS=/bbx/mount/n5ERGV8O49Zk88yXlx4Vk51Q4/661e5b3077313052c79383ea12f7e0a2aaea0e93ec405f9c96619038e981553d.fq.gz
+ CONTIGS=/bbx/output/contigs.fa
++ grep MemTotal: /proc/meminfo
++ tr -s ' '
++ cut -f 2 -d ' '
+ MEM_IN_KB=32946432
View mixed_effects.R
```{r}
library(lme4)
null <- glm.nb(gene_l1_norm ~ 1, data = data)
genome_null <- glm.nb(gene_l1_norm ~ biological_source_name, data = data)
n_misassemblies <- glm.nb(gene_l1_norm ~ n_misassemblies, data = data)
n_misassemblies_genome <- glmer.nb(gene_l1_norm ~ n_misassemblies + (1|biological_source_name), data = data)
View fail_codes.json
[
{
"abandon_library": 0,
"data_usable": 1,
"id": "PMO00001",
"jira_msg": "This library appears to be incorrectly scoped for the given project type. Please check the project parameters.",
"lab_action": "No Lab Action",
"segment_msg": "This library appears to be incorrectly scoped. Please check the project parameters.",
"sow_item": "Needs PMO Attention",
"type": "project"
View INSTALL.txt
Needs bitly/data_hacks
pip install --user data_hacks
View gist:996c0affbd32aae4b144

Quick Start Guide

The following is a step by step example of how to build a docker image that complies to the "bioboxes" standard which means only a small amount of code should have to be changed in order build customized assembly docker images. All the steps required to build and run a docker image should be included here but you should consult "bioboxes.org" for details.

If you use the minia assembler as an example, and follow these steps, you should be able to build and run the minia image without changing any code.

View gist:8ff0533ec20387c9c0a4
#!/usr/bin/env Rscript
# Assume that the libraries are installed in "../vendor/r/"
# Adjust this path to the relative path between the script
# and the packrat directory
set_package_environment <- function(args){
dir <- dirname(sub("--file=", "", args[grep("--file", args)]))
libs <- file.path(dir, "..", "vendor", "r", "packrat", "lib", "*", "*")
.libPaths(c(.libPaths(), libs))
View log.txt
++ mktemp -d
+ TMP_DIR=/tmp/tmp.jL0YC9HdH6
+ cd /tmp/tmp.jL0YC9HdH6
+ PROC=default
++ cut -f 2 -d :
++ egrep '^default:' /Procfile
+ CMD=' minia -in /inputs/reads.fq.gz -kmer-size 55 -abundance 5 -out genome'
+ [[ -z minia -in /inputs/reads.fq.gz -kmer-size 55 -abundance 5 -out genome ]]
+ eval minia -in /inputs/reads.fq.gz -kmer-size 55 -abundance 5 -out genome
++ minia -in /inputs/reads.fq.gz -kmer-size 55 -abundance 5 -out genome
View log.txt
This file has been truncated, but you can view the full file.
++ mktemp -d
+ TMP_DIR=/tmp/tmp.5CiDif8NjP
+ cd /tmp/tmp.5CiDif8NjP
+ PROC=default
++ cut -f 2 -d :
++ egrep '^default:' /Procfile
+ CMD=' gatb -p /inputs/reads.fq.gz --multik -o genome '
+ [[ -z gatb -p /inputs/reads.fq.gz --multik -o genome ]]
+ eval gatb -p /inputs/reads.fq.gz --multik -o genome
View gist:1de18382ed19d49dfafd
bind-key C-a last-window
bind-key C-c run-shell "tmux show-buffer | reattach-to-user-namespace pbcopy"
bind-key C-o rotate-window
bind-key C-v run-shell "reattach-to-user-namespace pbpaste | tmux load-buffer - && tmux paste-buffer"
bind-key C-z suspend-client
bind-key Space copy-mode
bind-key ! break-pane
bind-key " split-window
bind-key # list-buffers
bind-key $ command-prompt -I #S "rename-session '%%'"
@michaelbarton
michaelbarton / specification.mkd
Last active Aug 29, 2015
Specification for bioinformatics containers
View specification.mkd

Introduction

Purpose

The purpose of this document is provide a detailed specification for developers to write community-standardised bioinformatics containers. The audience of this document are bioinformaticians writing bioinformatics code that can be shared interchangeably using Linux containers. This document will describe the interfaces that a developer may expect to be available when the container is run.

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