Releases: hmgu-itg/burden_testing
Releases · hmgu-itg/burden_testing
Burden Testing v1.5.3
Burden Testing v1.5.2
Changes:
- Deleted singularity-deploy related files since remote building fails.
- Changed singularity definition file.
- Changed to compile HTSlib and BCFTools within
/opt
instead of/root
, since this might have the chance of saving unwanted files in the host root's directory. - Changed git cloning of htslib and bcftools to downloading the recommended source tarball to compile the two libraries, since the container was missing the htslib (tabix, bgzip) and bcftools executables so
prepare_regions.sh
was failing.
- Changed to compile HTSlib and BCFTools within
- Changes in
prepare_regions.sh
.- Refactored some code for improved readability.
- Used absolute paths in some
cd
commands during VEP build to fix VEP build. - Fixed incorrect URL for downloading VEP's
homo_sapiens_vep_98_GRCh38.tar.gz
cache file. - Added code to download GENCODE data from
http://
when download fails withftp://
- Changed fetching GENCODE data MD5 hash value with FTP to HTTP as fetching from FTP appears to hang in some environments (e.g. suanpan). Fetching with HTTP appeared more reliable across environments.
- Added code to fetch APPRIS file's MD5 hash and compare with the downloaded APPRIS file's MD5 hash
- Added Debug mode (
-m
), although not many debug messages added yet.
The run has been testing in suanpan
, but not yet on other environments.
Burden Testing v1.5.1
A collection of scripts for running burden testing pipeline.
Script version
This release corresponds to the scripted version of our burden testing pipeline. This was used in papers https://doi.org/10.1101/854752 and PMID 30405126. The scripts have been written and designed for the Sanger server infrastructure, be aware that quite a few paths will need changing if you wish to run this locally.