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jashapiro / get_ena_ftp.R
Last active Jun 30, 2020
An R function to get a table of ENA FTP urls for an SRA project
View get_ena_ftp.R
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 = ";")
}
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jashapiro / galaxy-delete_genomes.sh
Created Aug 16, 2012
Script to remove genomes from the default galaxy-indices file
View galaxy-delete_genomes.sh
# 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
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