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author | Justin S <3630356+codeandkey@users.noreply.github.com> | 2019-06-18 13:11:00 -0500 |
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committer | Peter Scheibel <scheibel1@llnl.gov> | 2019-06-18 11:11:00 -0700 |
commit | d82f8cd405c13d2fe4cfd4221669f1c3a5b023cb (patch) | |
tree | e24184a4ddc9a05f398b8dedf5670375594d1560 | |
parent | e35355f0402345f9649e919583617301ab34b138 (diff) | |
download | spack-d82f8cd405c13d2fe4cfd4221669f1c3a5b023cb.tar.gz spack-d82f8cd405c13d2fe4cfd4221669f1c3a5b023cb.tar.bz2 spack-d82f8cd405c13d2fe4cfd4221669f1c3a5b023cb.tar.xz spack-d82f8cd405c13d2fe4cfd4221669f1c3a5b023cb.zip |
repeatmasker: perl and HMMER dependency fixes (#11660)
repeatmasker depended on HMMER but was never actually configured to
use it. The package also had many shebangs pointing to random perl
locations, now patched to use Spack's perl installation.
-rw-r--r-- | var/spack/repos/builtin/packages/repeatmasker/package.py | 11 |
1 files changed, 11 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/repeatmasker/package.py b/var/spack/repos/builtin/packages/repeatmasker/package.py index bac7eb8377..e1c49d2cb0 100644 --- a/var/spack/repos/builtin/packages/repeatmasker/package.py +++ b/var/spack/repos/builtin/packages/repeatmasker/package.py @@ -4,6 +4,7 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +import glob class Repeatmasker(Package): @@ -71,6 +72,11 @@ class Repeatmasker(Package): self.spec['ncbi-rmblastn'].prefix.bin, 'Y']) + # set non-default HMMER search + config_answers.extend(['3', + self.spec['hmmer'].prefix, + 'N']) + # end configuration config_answers.append('5') @@ -83,4 +89,9 @@ class Repeatmasker(Package): perl = which('perl') perl('configure', input=f) + # fix perl paths + # every sbang points to perl, so a regex will suffice + for f in glob.glob('*.pm'): + filter_file('#!.*', '#!%s' % spec['perl'].command, f) + install_tree('.', prefix.bin) |