update recount-pump download.sh (yet again) to use sratoolkit 3.0.2 for both prefetch and fastq-dump.
The SRA file extension .sralite is now supported (beyond just the .sra file).
Outputs should still be backwards compatible with previous Pump runs, so no need to re-run Pump runs from before this.
Pump image now at 1.1.3
updated recount-pump download.sh (again) to use 1) sratoolkit 3.0.0 for downloading via prefetch to fix issues with dbGaP in 2.11.2
Outputs are still backwards compatible with previous Pump runs, so no need to re-run Pump runs from before this.
Pump image now at 1.1.1
updated recount-pump download.sh to use 1) sratoolkit 2.11.2 for downloading via prefetch to fix issues with 2.9.1 and the cloud 2) support limited download-from-S3 from within AWS (e.g. on an EC2 instance, download method is s3 instead of e.g. local). Also, the main Snakemake configuration file can be overridden from the command line by setting CONFIGFILE=/container/visible/path/to/monorail_config.json. This can be used to modify the download_exe setting to a user-developed script to support other download methods, e.g. {"download_exe":"/container/visible/path/to/my_download.sh"}.
Outputs are still backwards compatible with previous Pump runs, so no need to re-run Pump runs from before this.
Pump image now at 1.1.0
updated recount-unify's workflow.bash to support more than just human G026 annotation for gene sums checking via Megadepth (was hanging at this step for non-human organisms). Only applies to non-human organism Unifier runs (should not longer stall at check step).
Unifier image now at 1.1.1
fixed recount-unify's rejoin collision bug causing a number of genes to have wrong sums, update is not compatible with previous versions of the Unifier. Users should re-run unifier on all pump outputs with this release!
Unifier image now at 1.1.0
added post-run row count checks to Unifier
added some support for dbGaP runs via the docker/run_recount_unify.sh script