From 18b8cecdf69d9a6c9e63131fc8e5f0a9da276a64 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 21 May 2020 14:41:47 +0200 Subject: [PATCH 1/4] adding easyconfigs: Percolator-3.4-foss-2019a.eb, KyotoCabinet-1.2.77-GCCcore-8.2.0.eb --- .../KyotoCabinet-1.2.77-GCCcore-8.2.0.eb | 22 ++++++ .../p/Percolator/Percolator-3.4-foss-2019a.eb | 78 +++++++++++++++++++ 2 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/k/KyotoCabinet/KyotoCabinet-1.2.77-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/p/Percolator/Percolator-3.4-foss-2019a.eb diff --git a/easybuild/easyconfigs/k/KyotoCabinet/KyotoCabinet-1.2.77-GCCcore-8.2.0.eb b/easybuild/easyconfigs/k/KyotoCabinet/KyotoCabinet-1.2.77-GCCcore-8.2.0.eb new file mode 100644 index 000000000000..899fdd3d7441 --- /dev/null +++ b/easybuild/easyconfigs/k/KyotoCabinet/KyotoCabinet-1.2.77-GCCcore-8.2.0.eb @@ -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' diff --git a/easybuild/easyconfigs/p/Percolator/Percolator-3.4-foss-2019a.eb b/easybuild/easyconfigs/p/Percolator/Percolator-3.4-foss-2019a.eb new file mode 100644 index 000000000000..3c86a0368b96 --- /dev/null +++ b/easybuild/easyconfigs/p/Percolator/Percolator-3.4-foss-2019a.eb @@ -0,0 +1,78 @@ +# 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': 'foss', '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}" && ' +local_unpacked_dir_name = 'percolator-rel-%(version_major)s-0%(version_minor)s' +local_srcdir_root = '%%(builddir)s/%s/' % local_unpacked_dir_name + +github_account = 'percolator' +default_component_specs = { + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['rel-%(version_major)s-0%(version_minor)s.tar.gz'], + # can't use %(namelower)s here, because names are used to distinguish build dirs + 'start_dir': local_unpacked_dir_name, + 'checksums': ['ee094039b60aa2e2e15ec8228da087328ca523fa73b89cd69721621eb219cf4d'], + # by default, CMakeMake will (re)use %(builddir)s/easybuild_obj, which causes trouble + # manually create build folders in each component (by name) + 'separate_build_dir': False, + 'preconfigopts': + 'mkdir easybuild_obj/%%(namelower)s -p && cd easybuild_obj/%%(namelower)s && %s' % local_sw_preconfigopts, + 'prebuildopts': "cd easybuild_obj/%(namelower)s && ", + 'preinstallopts': "cd easybuild_obj/%(namelower)s && ", +} + +components = [ + (name, version, { + # Create and use custom builddir + 'configopts': '-DTARGET_ARCH=x86_64 -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': '-DTARGET_ARCH=x86_64 -DSERIALIZE="KyotoCabinet" ', + 'srcdir': '%s/src/converters' % local_srcdir_root, + }), + ('%s_elude_tool' % name, version, { + 'configopts': '-DTARGET_ARCH=x86_64 ', + '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' From 181f10ec8abeda5024e54bb6596c1a9e8c3db2f0 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Mon, 25 May 2020 10:18:47 +0200 Subject: [PATCH 2/4] changed toolchain, fixed comment position. --- ...olator-3.4-foss-2019a.eb => Percolator-3.4-gompi-2019a.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/Percolator/{Percolator-3.4-foss-2019a.eb => Percolator-3.4-gompi-2019a.eb} (95%) diff --git a/easybuild/easyconfigs/p/Percolator/Percolator-3.4-foss-2019a.eb b/easybuild/easyconfigs/p/Percolator/Percolator-3.4-gompi-2019a.eb similarity index 95% rename from easybuild/easyconfigs/p/Percolator/Percolator-3.4-foss-2019a.eb rename to easybuild/easyconfigs/p/Percolator/Percolator-3.4-gompi-2019a.eb index 3c86a0368b96..04c9e1f2f8fd 100644 --- a/easybuild/easyconfigs/p/Percolator/Percolator-3.4-foss-2019a.eb +++ b/easybuild/easyconfigs/p/Percolator/Percolator-3.4-gompi-2019a.eb @@ -12,7 +12,7 @@ version = '3.4' homepage = 'https://github.com/percolator/percolator' description = "Semi-supervised learning for peptide identification from shotgun proteomics datasets" -toolchain = {'name': 'foss', 'version': '2019a'} +toolchain = {'name': 'gompi', 'version': '2019a'} builddependencies = [ ('CMake', '3.13.3'), @@ -32,6 +32,7 @@ dependencies = [ default_easyblock = 'CMakeMake' local_sw_preconfigopts = 'export XSDDIR="${EBROOTXSD}" && export XERCESCROOT="${EBROOTXERCESMINCPLUSPLUS}" && ' +# can't use %(namelower)s below, because names are used to distinguish build dirs local_unpacked_dir_name = 'percolator-rel-%(version_major)s-0%(version_minor)s' local_srcdir_root = '%%(builddir)s/%s/' % local_unpacked_dir_name @@ -39,7 +40,6 @@ github_account = 'percolator' default_component_specs = { 'source_urls': [GITHUB_LOWER_SOURCE], 'sources': ['rel-%(version_major)s-0%(version_minor)s.tar.gz'], - # can't use %(namelower)s here, because names are used to distinguish build dirs 'start_dir': local_unpacked_dir_name, 'checksums': ['ee094039b60aa2e2e15ec8228da087328ca523fa73b89cd69721621eb219cf4d'], # by default, CMakeMake will (re)use %(builddir)s/easybuild_obj, which causes trouble From 3ce85cb7b3f72be6b97f454b80c5baff308bc4e0 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Tue, 26 May 2020 09:00:21 +0200 Subject: [PATCH 3/4] fixed hardcoded values --- .../easyconfigs/p/Percolator/Percolator-3.4-gompi-2019a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Percolator/Percolator-3.4-gompi-2019a.eb b/easybuild/easyconfigs/p/Percolator/Percolator-3.4-gompi-2019a.eb index 04c9e1f2f8fd..d5e08a6b48fc 100644 --- a/easybuild/easyconfigs/p/Percolator/Percolator-3.4-gompi-2019a.eb +++ b/easybuild/easyconfigs/p/Percolator/Percolator-3.4-gompi-2019a.eb @@ -54,17 +54,17 @@ default_component_specs = { components = [ (name, version, { # Create and use custom builddir - 'configopts': '-DTARGET_ARCH=x86_64 -DXML_SUPPORT=ON ', + 'configopts': '-DTARGET_ARCH=%(arch)s -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': '-DTARGET_ARCH=x86_64 -DSERIALIZE="KyotoCabinet" ', + 'configopts': '-DTARGET_ARCH=%(arch)s -DSERIALIZE="KyotoCabinet" ', 'srcdir': '%s/src/converters' % local_srcdir_root, }), ('%s_elude_tool' % name, version, { - 'configopts': '-DTARGET_ARCH=x86_64 ', + 'configopts': '-DTARGET_ARCH=%(arch)s ', 'srcdir': '%s/src/elude_tool' % local_srcdir_root, }), ] From 9818e82a04fda5eb5a67dcf224178dd3d3549042 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Fri, 5 Jun 2020 09:37:20 +0200 Subject: [PATCH 4/4] fixed remarks --- .../p/Percolator/Percolator-3.4-gompi-2019a.eb | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/Percolator/Percolator-3.4-gompi-2019a.eb b/easybuild/easyconfigs/p/Percolator/Percolator-3.4-gompi-2019a.eb index d5e08a6b48fc..6922c8e98661 100644 --- a/easybuild/easyconfigs/p/Percolator/Percolator-3.4-gompi-2019a.eb +++ b/easybuild/easyconfigs/p/Percolator/Percolator-3.4-gompi-2019a.eb @@ -32,9 +32,10 @@ dependencies = [ default_easyblock = 'CMakeMake' local_sw_preconfigopts = 'export XSDDIR="${EBROOTXSD}" && export XERCESCROOT="${EBROOTXERCESMINCPLUSPLUS}" && ' -# can't use %(namelower)s below, because names are used to distinguish build dirs +# 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 = { @@ -42,29 +43,22 @@ default_component_specs = { 'sources': ['rel-%(version_major)s-0%(version_minor)s.tar.gz'], 'start_dir': local_unpacked_dir_name, 'checksums': ['ee094039b60aa2e2e15ec8228da087328ca523fa73b89cd69721621eb219cf4d'], - # by default, CMakeMake will (re)use %(builddir)s/easybuild_obj, which causes trouble - # manually create build folders in each component (by name) - 'separate_build_dir': False, - 'preconfigopts': - 'mkdir easybuild_obj/%%(namelower)s -p && cd easybuild_obj/%%(namelower)s && %s' % local_sw_preconfigopts, - 'prebuildopts': "cd easybuild_obj/%(namelower)s && ", - 'preinstallopts': "cd easybuild_obj/%(namelower)s && ", + 'preconfigopts': local_sw_preconfigopts } components = [ (name, version, { - # Create and use custom builddir - 'configopts': '-DTARGET_ARCH=%(arch)s -DXML_SUPPORT=ON ', + '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': '-DTARGET_ARCH=%(arch)s -DSERIALIZE="KyotoCabinet" ', + 'configopts': local_common_configopts + '-DSERIALIZE="KyotoCabinet" ', 'srcdir': '%s/src/converters' % local_srcdir_root, }), ('%s_elude_tool' % name, version, { - 'configopts': '-DTARGET_ARCH=%(arch)s ', + 'configopts': local_common_configopts, 'srcdir': '%s/src/elude_tool' % local_srcdir_root, }), ]