14fa5850fa5c
Update
author | Steve Losh <steve@stevelosh.com> |
---|---|
date | Sat, 01 Feb 2020 21:11:46 -0500 |
parents | c42b3cb28bc0 |
children | e5379ae202a9 |
branches/tags | (none) |
files | README.markdown |
Changes
--- a/README.markdown Sat Feb 01 15:22:36 2020 -0500 +++ b/README.markdown Sat Feb 01 21:11:46 2020 -0500 @@ -333,3 +333,14 @@ Attempted to figure out how to acquire MS Word for the class. Apparently there's a web version of Word now? If I can use that, at least I won't have to spin up a full Windows VM to write the papers… + +Installed `sra-toolkit` from Ubuntu's repository. Unfortunately it doesn't seem +to come with `fasterq-dump`, only the older `fastq-dump`, at least according to +`dpkg-query -L sra-toolkit`. Installed the latest binary from their site +instead. + +Poked around at both `fastq-dump` and `fasterq-dump`. `fasterq-dump` seems more +documented and user friendly, and is definitely faster. The biggest speedup +came from telling it to use RAM as its temporary filesystem with `-t /dev/shm`, +which cut the time down to 1/3. Guess all this RAM *is* actually good for +something.