zhangyiss/spack
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

gatk: updating and expanding java dependency (#30476)

Browse Source
This commit is contained in:
snehring 2022-05-04 12:51:44 -05:00 committed by GitHub
parent b7f33fb393
commit e24373f262
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
1 changed files with 4 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
var/spack/repos/builtin/packages/gatk/package.py
View File

@ -15,7 +15,9 @@ class Gatk(Package):
homepage = "https://gatk.broadinstitute.org/hc/en-us" homepage = "https://gatk.broadinstitute.org/hc/en-us"
url = "https://github.com/broadinstitute/gatk/releases/download/4.2.2.0/gatk-4.2.2.0.zip" url = "https://github.com/broadinstitute/gatk/releases/download/4.2.2.0/gatk-4.2.2.0.zip"
list_url = "https://github.com/broadinstitute/gatk/releases" list_url = "https://github.com/broadinstitute/gatk/releases"
maintainers = ['snehring']
version('4.2.6.1', sha256='1125cfc862301d437310506c8774d36c3a90d00d52c7b5d6b59dac7241203628')
version('4.2.2.0', sha256='ddd902441d1874493796566159288e9df178714ac18216ba05092136db1497fd') version('4.2.2.0', sha256='ddd902441d1874493796566159288e9df178714ac18216ba05092136db1497fd')
version('4.1.8.1', sha256="42e6de5059232df1ad5785c68c39a53dc1b54afe7bb086d0129f4dc95fb182bc") version('4.1.8.1', sha256="42e6de5059232df1ad5785c68c39a53dc1b54afe7bb086d0129f4dc95fb182bc")
version('4.1.8.0', sha256="3ce1c2a15c44d0cfc9b2c26111f4518c215a5f9314072b4eb61f07ab5d01eef6") version('4.1.8.0', sha256="3ce1c2a15c44d0cfc9b2c26111f4518c215a5f9314072b4eb61f07ab5d01eef6")
@ -48,7 +50,7 @@ class Gatk(Package):
# output. # output.
variant('r', default=False, description='Use R for plotting') variant('r', default=False, description='Use R for plotting')
depends_on("java@8", type="run") depends_on("java@8:", type="run")
depends_on("python@2.6:2.8,3.6:", type="run", when="@4.0:") depends_on("python@2.6:2.8,3.6:", type="run", when="@4.0:")
depends_on("r@3.2:", type="run", when="@4.0: +r") depends_on("r@3.2:", type="run", when="@4.0: +r")
@ -62,6 +64,7 @@ def install(self, spec, prefix):
# Skip helper script for versions >4.0 # Skip helper script for versions >4.0
if spec.satisfies("@4.0:"): if spec.satisfies("@4.0:"):
set_executable('gatk')
install("gatk", prefix.bin) install("gatk", prefix.bin)
else: else:
# Set up a helper script to call java on the jar file, # Set up a helper script to call java on the jar file,