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Changes to Docker material #270

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merged 23 commits into from
Nov 15, 2024
Merged

Changes to Docker material #270

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f526e98
Remove MAINTAINER label from Dockerfiles
fasterius Nov 12, 2024
99795d2
Add note on OCI Docker label best practices
fasterius Nov 12, 2024
31bff6c
Fix naming of Dockerfiles according to conventions
fasterius Nov 12, 2024
c215721
Harmonise Dockerfile formatting
fasterius Nov 12, 2024
19e9a0f
Fix naming of `linux/amd64` platform specification
fasterius Nov 12, 2024
c32405b
Add missing note title word
fasterius Nov 12, 2024
a58e880
Streamline `[slim/conda].Dockerfile` files
fasterius Nov 12, 2024
a5b23f3
Streamline final tutorial Dockerfile
fasterius Nov 12, 2024
d17a01a
Add extra material for multi-stage Docker builds
fasterius Nov 13, 2024
1682dd0
Fix broken Docker image
fasterius Nov 13, 2024
bcd97a5
Minor updates to conform to build checks
johnne Nov 13, 2024
461337b
Fix CMD line of Dockerfile
johnne Nov 14, 2024
c6cca74
Add SHELL instruction
johnne Nov 14, 2024
0994714
Fix embedding of resources in Quarto document
fasterius Nov 14, 2024
9324734
Set SHELL to not require JSON format for CMD
johnne Nov 14, 2024
e3e8b14
Fix embed-resources
johnne Nov 14, 2024
a1668fe
Move callout for ARM users
johnne Nov 14, 2024
d74046a
Merge branch 'docker-changes' of github.com:NBISweden/workshop-reprod…
johnne Nov 14, 2024
837c4c3
Remove section on jupyter notebook with Docker
johnne Nov 14, 2024
1fc4dad
Remove expose part from Dockerfile
johnne Nov 14, 2024
11805cf
Make supplementary table less redundant
johnne Nov 15, 2024
9365c3b
Fix minor formatting and spelling errors
johnne Nov 15, 2024
61d1b4a
Give explicit name for multi-stage Dockerfile
johnne Nov 15, 2024
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27 changes: 16 additions & 11 deletions tutorials/containers/code/supplementary_material.qmd
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I modified the code here to make the sample table less cluttered. There used to be 2 lines for each sample due to the info in gsm$characteristics_ch1. Now we extract the treatment: and growth phase info and put in separate columns, resulting in a condensed table.

Original file line number Diff line number Diff line change
Expand Up @@ -54,22 +54,29 @@ colnames(counts_summary) <- gsub(".*(SRR[0-9]+)\\..*", "\\1",
meta <- data.frame()
for (GSM in gsm_ids) {
gsm <- Meta(getGEO(GSM))
current_meta <- as.data.frame(do.call(cbind, gsm))
current_meta <- as.data.frame(
list(
title=gsm$title, geo_accession=gsm$geo_accession, source_name_ch1=gsm$source_name_ch1,
growth_phase=gsub("growth phase: ", "", gsm$characteristics_ch1[grep("growth phase", gsm$characteristics_ch1)]),
treatment=gsub("treatment: ", "", gsm$characteristics_ch1[grep("treatment", gsm$characteristics_ch1)])
)
)
meta <- rbind(meta, current_meta)
}
meta <- meta[c("title", "geo_accession", "source_name_ch1", "characteristics_ch1")]
meta <- meta[c("title", "geo_accession", "source_name_ch1", "growth_phase", "treatment")]
gsm2srr <- data.frame(geo_accession = gsm_ids, SRR = srr_ids)
meta <- merge(meta, gsm2srr, by = "geo_accession")

# Read FastQC data and update column names
qc <- read.delim(multiqc_file)
patterns <- c(".+percent_duplicates.*",
".+percent_gc.*",
".+avg_sequence_length.*",
".+percent_fails.*",
".+total_sequences.*")
patterns <- c("*.+percent_duplicates.*",
"*.+percent_gc.*",
"*.+avg_sequence_length.*",
"*.+median_sequence_length.*",
"*.+percent_fails.*",
"*.+total_sequences.*")
subs <- c("Percent duplicates", "Percent GC", "Avg sequence length",
"Percent fails", "Total sequences")
"Median sequence length", "Percent fails", "Total sequences")
for (i in 1:length(patterns)) {
colnames(qc) <- gsub(patterns[i], subs[i], colnames(qc))
}
Expand All @@ -85,10 +92,8 @@ was aligned and counted.
# Supplementary Tables and Figures

```{r Sample info}
columns <- c("SRR", "geo_accession", "source_name_ch1", "characteristics_ch1")
columns <- c("SRR", "geo_accession", "source_name_ch1", "growth_phase", "treatment")
sample_info <- meta[, columns]
sample_info$characteristics_ch1 <- gsub("treatment: ", "", sample_info$characteristics_ch1)
sample_info$characteristics_ch1 <- gsub("growth phase: ", "", sample_info$characteristics_ch1)
sample_info
```

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