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Burden Testing v1.5.2
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@youngchanpark youngchanpark released this 13 Jul 02:54
· 19 commits to stable since this release
v1.5.2
62b479f

Changes:

  1. Deleted singularity-deploy related files since remote building fails.
  2. 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.
  3. 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 with ftp://
    • 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.

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