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fastqc: Use the spack built perl (#35276)

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The fastqc script was using the system perl. This PR sets the script to
use the spack built/provided perl. This PR also removes the code that
adds the java path. That should be handled by module loading as far as I
know.
This commit is contained in:
Glenn Johnson 2023-02-01 11:47:10 -06:00 committed by GitHub
parent 448bd31c87
commit eac04af0e7
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1 changed files with 3 additions and 8 deletions
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11
var/spack/repos/builtin/packages/fastqc/package.py
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@ -22,6 +22,9 @@ class Fastqc(Package):
patch("fastqc.patch", level=0) patch("fastqc.patch", level=0)
def patch(self):
filter_file("/usr/bin/perl", self.spec["perl"].command.path, "fastqc", backup=False)
def install(self, spec, prefix): def install(self, spec, prefix):
mkdir(prefix.bin) mkdir(prefix.bin)
mkdir(prefix.lib) mkdir(prefix.lib)
@ -32,11 +35,3 @@ def install(self, spec, prefix):
install_tree(d, join_path(prefix.lib, d)) install_tree(d, join_path(prefix.lib, d))
chmod = which("chmod") chmod = which("chmod")
chmod("+x", prefix.bin.fastqc) chmod("+x", prefix.bin.fastqc)
# In theory the 'run' dependency on 'jdk' above should take
# care of this for me. In practice, it does not.
def setup_run_environment(self, env):
"""Add <prefix> to the path; the package has a script at the
top level.
"""
env.prepend_path("PATH", self.spec["java"].prefix.bin)