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jashapiro / galaxy-delete_genomes.sh
Created August 16, 2012 17:33
Script to remove genomes from the default galaxy-indices file
# removing files from galaxyIndices that we don't need.
# I'm going to create a very minimal version; no vertebrates
declare -a DELETE_GENOMES=(
blastdb/htgs
blastdb/wgs
Amellifera_Honeybee
Athaliana
Btaurus
Celegans/WS200
@jashapiro
jashapiro / keybase.md
Created February 26, 2016 16:13

Keybase proof

I hereby claim:

  • I am jashapiro on github.
  • I am jashapiro (https://keybase.io/jashapiro) on keybase.
  • I have a public key ASCSbMp9DRc1hDGv-HZEDtfwPxUIqO9EJTGSgtq1p7KTSQo

To claim this, I am signing this object:

@jashapiro
jashapiro / get_ena_ftp.R
Last active June 30, 2020 12:52
An R function to get a table of ENA FTP urls for an SRA project
get_ena_ftp <- function(SRA_project){
ena_url <- stringr::str_interp("http://www.ebi.ac.uk/ena/data/warehouse/filereport?accession=${SRA_project}&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes")
ena_table <- readr::read_tsv(ena_url) %>%
tidyr::separate_rows(fastq_ftp, fastq_md5, fastq_bytes, sep = ";")
}
@jashapiro
jashapiro / test.rmd
Last active March 15, 2021 20:49
Test rmarkdown::render()
---
title: "Test"
output: html_notebook
---
Make some vectors
```{r}
abc <- c("a", "b", "c")
nums <- 1:3