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{bio,lib}[GCCcore/8.2.0,foss/2019a] Percolator v3.4, KyotoCabinet v1.2.77 #10665

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Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
easyblock = 'ConfigureMake'

name = 'KyotoCabinet'
version = '1.2.77'

homepage = 'https://fallabs.com/kyotocabinet'
description = "Kyoto Cabinet is a library of routines for managing a database."

toolchain = {'name': 'GCCcore', 'version': '8.2.0'}

source_urls = ['https://fallabs.com/kyotocabinet/pkg/']
sources = [SOURCELOWER_TAR_GZ]
checksums = ['56899329384cc6f0f1f8aa3f1b41001071ca99c1d79225086a7f3575c0209de6']

builddependencies = [('binutils', '2.31.1')]

sanity_check_paths = {
'files': ['bin/kcdirmgr', 'bin/kcdirtest', 'bin/kcstashtest', 'bin/kcpolymgr', 'bin/kcpolytest'],
'dirs': [],
}

moduleclass = 'lib'
72 changes: 72 additions & 0 deletions easybuild/easyconfigs/p/Percolator/Percolator-3.4-gompi-2019a.eb
Original file line number Diff line number Diff line change
@@ -0,0 +1,72 @@
# Author: Pavel Grochal (INUITS)
# License: GPLv2

easyblock = 'Bundle'

name = 'Percolator'
version = '3.4'

# homepage doesn't have correctly working https
# stating GitHub because landing page links the homepage
# http://percolator.ms/
homepage = 'https://github.com/percolator/percolator'
description = "Semi-supervised learning for peptide identification from shotgun proteomics datasets"

toolchain = {'name': 'gompi', 'version': '2019a'}

builddependencies = [
('CMake', '3.13.3'),
('cURL', '7.63.0'),
]

dependencies = [
('zlib', '1.2.11'),
('Boost', '1.70.0'),
('KyotoCabinet', '1.2.77'),
('SQLite', '3.27.2'),
('bzip2', '1.0.6'),
('Xerces-C++', '3.2.2'),
('XSD', '4.0.0'),
]

default_easyblock = 'CMakeMake'

local_sw_preconfigopts = 'export XSDDIR="${EBROOTXSD}" && export XERCESCROOT="${EBROOTXERCESMINCPLUSPLUS}" && '
# can't use %(namelower)s below, because names are derived from components
local_unpacked_dir_name = 'percolator-rel-%(version_major)s-0%(version_minor)s'
local_srcdir_root = '%%(builddir)s/%s/' % local_unpacked_dir_name
local_common_configopts = '-DTARGET_ARCH=%(arch)s '

github_account = 'percolator'
default_component_specs = {
'source_urls': [GITHUB_LOWER_SOURCE],
'sources': ['rel-%(version_major)s-0%(version_minor)s.tar.gz'],
'start_dir': local_unpacked_dir_name,
'checksums': ['ee094039b60aa2e2e15ec8228da087328ca523fa73b89cd69721621eb219cf4d'],
'preconfigopts': local_sw_preconfigopts
}

components = [
(name, version, {
'configopts': local_common_configopts + '-DXML_SUPPORT=ON ',
'srcdir': local_srcdir_root,
}),
('%s_converters' % name, version, {
# Installation docs states using "TokyoCabinet" but from all information obtained
# TokyoCabinet and KyotoCabinet should be different implementations of the same protocol.
'configopts': local_common_configopts + '-DSERIALIZE="KyotoCabinet" ',
'srcdir': '%s/src/converters' % local_srcdir_root,
}),
('%s_elude_tool' % name, version, {
'configopts': local_common_configopts,
'srcdir': '%s/src/elude_tool' % local_srcdir_root,
}),
]

sanity_check_paths = {
'files': ['bin/percolator'],
'dirs': ['share/xml/percolator/'],
}
sanity_check_commands = ['percolator --help']

moduleclass = 'bio'