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| author | Glenn Johnson <glenn-johnson@uiowa.edu> | 2023-02-01 11:47:10 -0600 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2023-02-01 09:47:10 -0800 |
| commit | eac04af0e79dc5ceb0b89b81798b0bf4fa58a862 (patch) | |
| tree | a65a753b9a983e927ba2b5dd82056288dade944f | |
| parent | 448bd31c8758737f84fa9522f185c171e37e7ed5 (diff) | |
| download | spack-eac04af0e79dc5ceb0b89b81798b0bf4fa58a862.tar.gz spack-eac04af0e79dc5ceb0b89b81798b0bf4fa58a862.tar.bz2 spack-eac04af0e79dc5ceb0b89b81798b0bf4fa58a862.tar.xz spack-eac04af0e79dc5ceb0b89b81798b0bf4fa58a862.zip | |
fastqc: Use the spack built perl (#35276)
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.
| -rw-r--r-- | var/spack/repos/builtin/packages/fastqc/package.py | 11 |
1 files changed, 3 insertions, 8 deletions
diff --git a/var/spack/repos/builtin/packages/fastqc/package.py b/var/spack/repos/builtin/packages/fastqc/package.py index ff79d7b0c5..247c00dab7 100644 --- a/var/spack/repos/builtin/packages/fastqc/package.py +++ b/var/spack/repos/builtin/packages/fastqc/package.py @@ -22,6 +22,9 @@ class Fastqc(Package): 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): mkdir(prefix.bin) mkdir(prefix.lib) @@ -32,11 +35,3 @@ class Fastqc(Package): install_tree(d, join_path(prefix.lib, d)) chmod = which("chmod") 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) |