From 575af9e8b402afddeee0560be4da23d945fcd407 Mon Sep 17 00:00:00 2001 From: software Date: Mon, 21 Oct 2024 09:21:51 +0000 Subject: [PATCH 1/3] adding easyconfigs: snptest-2.5.6.eb --- .../easyconfigs/s/snptest/snptest-2.5.6.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/snptest/snptest-2.5.6.eb diff --git a/easybuild/easyconfigs/s/snptest/snptest-2.5.6.eb b/easybuild/easyconfigs/s/snptest/snptest-2.5.6.eb new file mode 100644 index 00000000000..8c1a46c08dc --- /dev/null +++ b/easybuild/easyconfigs/s/snptest/snptest-2.5.6.eb @@ -0,0 +1,31 @@ +easyblock = 'Tarball' + +name = 'snptest' +version = '2.5.6' + +homepage = 'https://www.chg.ox.ac.uk/~gav/snptest/' +description = """SNPTEST is a program for the analysis of single SNP association in genome-wide studies. + The tests implemented include + + Binary (case-control) phenotypes, single and multiple quantitative phenotypes + Bayesian and Frequentist tests + Ability to condition upon an arbitrary set of covariates and/or SNPs. + Various different methods for the dealing with imputed SNPs. +""" + +toolchain = SYSTEM + +source_urls = ['https://www.well.ox.ac.uk/~gav/resources/'] +sources = ['snptest_v2.5.6_CentOS_Linux7.8-x86_64_dynamic.tgz'] +checksums = ['c2c829def961dd2f6377c388d8aa22cab17945961c47e39c4a94493466c0a52e'] + +sanity_check_paths = { + 'files': ['LICENCE'], + 'dirs': ['doc', 'example'], +} + +modextrapaths = {'PATH': ''} + +sanity_check_commands = ["snptest_v2.5.6 -help"] + +moduleclass = 'bio' From d52cd0bc32e41a747e6f8fc2d65ec09f1652f8bb Mon Sep 17 00:00:00 2001 From: software Date: Mon, 21 Oct 2024 15:35:55 +0000 Subject: [PATCH 2/3] Use uppercase naming and add unversioned symlink to the binary --- .../easyconfigs/s/SNPTEST/SNPTEST-2.5.6.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/s/SNPTEST/SNPTEST-2.5.6.eb diff --git a/easybuild/easyconfigs/s/SNPTEST/SNPTEST-2.5.6.eb b/easybuild/easyconfigs/s/SNPTEST/SNPTEST-2.5.6.eb new file mode 100644 index 00000000000..a404d99e468 --- /dev/null +++ b/easybuild/easyconfigs/s/SNPTEST/SNPTEST-2.5.6.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'SNPTEST' +version = '2.5.6' + +homepage = 'https://www.chg.ox.ac.uk/~gav/snptest/' +description = """SNPTEST is a program for the analysis of single SNP association in genome-wide studies. + The tests implemented include + + Binary (case-control) phenotypes, single and multiple quantitative phenotypes + Bayesian and Frequentist tests + Ability to condition upon an arbitrary set of covariates and/or SNPs. + Various different methods for the dealing with imputed SNPs. +""" + +toolchain = SYSTEM + +source_urls = ['https://www.well.ox.ac.uk/~gav/resources/'] +sources = ['snptest_v2.5.6_CentOS_Linux7.8-x86_64_dynamic.tgz'] +checksums = ['c2c829def961dd2f6377c388d8aa22cab17945961c47e39c4a94493466c0a52e'] + +postinstallcmds = ["cd %(installdir)s && ln -s snptest_v2.5.6 snptest"] + +sanity_check_paths = { + 'files': ['LICENCE'], + 'dirs': ['doc', 'example'], +} + +modextrapaths = {'PATH': ''} + +sanity_check_commands = ["snptest -help"] + +moduleclass = 'bio' From 3950c50851f9958fe0e619ae5190d274eb7a029b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 21 Oct 2024 16:38:47 +0100 Subject: [PATCH 3/3] Delete easybuild/easyconfigs/s/snptest/snptest-2.5.6.eb --- .../easyconfigs/s/snptest/snptest-2.5.6.eb | 31 ------------------- 1 file changed, 31 deletions(-) delete mode 100644 easybuild/easyconfigs/s/snptest/snptest-2.5.6.eb diff --git a/easybuild/easyconfigs/s/snptest/snptest-2.5.6.eb b/easybuild/easyconfigs/s/snptest/snptest-2.5.6.eb deleted file mode 100644 index 8c1a46c08dc..00000000000 --- a/easybuild/easyconfigs/s/snptest/snptest-2.5.6.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'Tarball' - -name = 'snptest' -version = '2.5.6' - -homepage = 'https://www.chg.ox.ac.uk/~gav/snptest/' -description = """SNPTEST is a program for the analysis of single SNP association in genome-wide studies. - The tests implemented include - - Binary (case-control) phenotypes, single and multiple quantitative phenotypes - Bayesian and Frequentist tests - Ability to condition upon an arbitrary set of covariates and/or SNPs. - Various different methods for the dealing with imputed SNPs. -""" - -toolchain = SYSTEM - -source_urls = ['https://www.well.ox.ac.uk/~gav/resources/'] -sources = ['snptest_v2.5.6_CentOS_Linux7.8-x86_64_dynamic.tgz'] -checksums = ['c2c829def961dd2f6377c388d8aa22cab17945961c47e39c4a94493466c0a52e'] - -sanity_check_paths = { - 'files': ['LICENCE'], - 'dirs': ['doc', 'example'], -} - -modextrapaths = {'PATH': ''} - -sanity_check_commands = ["snptest_v2.5.6 -help"] - -moduleclass = 'bio'