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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 /var | |
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.
Diffstat (limited to 'var')
-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) |