From 6df1b509fa32964e05d0cde5a55ae4a1281aa91c Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Tue, 6 Apr 2021 01:35:51 -0500 Subject: repeatmasker: update and fix package (#22785) - version 4.0.7 was not building - version 4.0.9 was not setting search correctly due to an extra "return" in config - added version 4.1.2-p1 - new version needs py-h5py - new version does not need utf8 patch - url format changed --- .../repos/builtin/packages/repeatmasker/package.py | 35 ++++++++++++++-------- 1 file changed, 23 insertions(+), 12 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/repeatmasker/package.py b/var/spack/repos/builtin/packages/repeatmasker/package.py index 30da0679fc..3663f57b4d 100644 --- a/var/spack/repos/builtin/packages/repeatmasker/package.py +++ b/var/spack/repos/builtin/packages/repeatmasker/package.py @@ -12,8 +12,8 @@ class Repeatmasker(Package): repeats and low complexity DNA sequences.""" homepage = "http://www.repeatmasker.org" - url = "http://www.repeatmasker.org/RepeatMasker-open-4-0-7.tar.gz" + version('4.1.2-p1', sha256='4be54bf6c050422b211e24a797feb06fd7954c8b4ee6f3ece94cb6faaf6b0e96') version('4.0.9', sha256='8d67415d89ed301670b7632ea411f794c6e30d8ed0f007a726c4b0a39c8638e5') version('4.0.7', sha256='16faf40e5e2f521146f6692f09561ebef5f6a022feb17031f2ddb3e3aabcf166') @@ -25,15 +25,21 @@ class Repeatmasker(Package): depends_on('hmmer') depends_on('ncbi-rmblastn') depends_on('trf') + depends_on('python', when='@4.1:', type=('build', 'run')) + depends_on('py-h5py', when='@4.1:', type=('build', 'run')) depends_on('phrap-crossmatch-swat', type=('build', 'run'), when='+crossmatch') - patch('utf8.patch') + patch('utf8.patch', when='@:4.0') def url_for_version(self, version): - url = 'http://www.repeatmasker.org/RepeatMasker-open-{0}.tar.gz' - return url.format(version.dashed) + if version >= Version('4.1.0'): + url = 'http://www.repeatmasker.org/RepeatMasker/RepeatMasker-{0}.tar.gz' + return url.format(version) + else: + url = 'http://www.repeatmasker.org/RepeatMasker/RepeatMasker-open-{0}.tar.gz' + return url.format(version.dashed) def install(self, spec, prefix): # Config questions consist of: @@ -55,14 +61,14 @@ class Repeatmasker(Package): config_answers = [] - if spec.satisfies('@4.0.9:'): + if spec.satisfies('@:4.0.7'): # 4.0.9 removes a bunch of the interactive options - config_answers.append('') - else: config_answers.extend(['', self.spec['perl'].command.path, - self.stage.source_path, - self.spec['trf'].prefix.bin.trf]) + self.stage.source_path]) + + # set path to trf + config_answers.append(self.spec['trf'].prefix.bin.trf) # add crossmatch search if '+crossmatch' in spec: @@ -75,9 +81,14 @@ class Repeatmasker(Package): 'Y']) # set non-default HMMER search - config_answers.extend(['3', - self.spec['hmmer'].prefix, - 'N']) + if spec.satisfies('@4.0.9:'): + config_answers.extend(['3', + self.spec['hmmer'].prefix.bin, + 'N']) + else: + config_answers.extend(['4', + self.spec['hmmer'].prefix.bin, + 'N']) # end configuration config_answers.append('5') -- cgit v1.2.3-60-g2f50