diff --git a/easybuild/easyconfigs/h/HOMER/HOMER-4.11-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/h/HOMER/HOMER-4.11-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..49de16a3d995 --- /dev/null +++ b/easybuild/easyconfigs/h/HOMER/HOMER-4.11-foss-2023a-R-4.3.2.eb @@ -0,0 +1,49 @@ +easyblock = 'Binary' + +name = 'HOMER' +version = '4.11' +versionsuffix = '-R-%(rver)s' + +homepage = "http://homer.ucsd.edu/homer/" +description = """HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and + next-gen sequencing analysis. It is a collection of command line programs for unix-style operating systems written + in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding + 8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, + RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['http://homer.ucsd.edu/homer'] +sources = ['configureHomer.pl'] +checksums = ['ccdaa3004a0e0df0882634671d4a1acc88364761e0e6c7ea329ebbf1eb729537'] + +builddependencies = [ + ('wget', '1.24.5'), + ('Zip', '3.0'), + ('UnZip', '6.0'), +] + +dependencies = [ + ('Perl', '5.36.1'), + ('R', '4.3.2'), + ('SAMtools', '1.18'), + ('R-bundle-Bioconductor', '3.18', versionsuffix) +] + +postinstallcmds = ["cd %(installdir)s && perl ./configureHomer.pl -install homer -version v%(version)s"] + +sanity_check_paths = { + 'files': [ + 'bin/homer', + 'bin/getGenomeTilingPeaks', + 'config.txt', + 'DoughnutDocumentation.pdf', + 'data/accession/homologene.data', + 'motifs/hnf1b.motif', + ], + 'dirs': ['bin', 'data', 'motifs', 'update'], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.7-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..30a2e4a26f2f --- /dev/null +++ b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.7-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libidn2' +version = '2.3.7' + +homepage = 'http://www.gnu.org/software/%(name)s' +description = "Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftp.gnu.org/gnu/libidn/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4c21a791b610b9519b9d0e12b8097bf2f359b12f8dd92647611a929e6bfd7d64'] + +builddependencies = [ + ('binutils', '2.40'), +] + + +sanity_check_paths = { + 'files': ['bin/idn2', 'lib/%s.%s' % (name, SHLIB_EXT)], + 'dirs': ['include'], +} + +sanity_check_commands = ['idn2 --help'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wget/wget-1.24.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/w/wget/wget-1.24.5-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..ea4438bce14b --- /dev/null +++ b/easybuild/easyconfigs/w/wget/wget-1.24.5-GCCcore-12.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'wget' +version = '1.24.5' + +homepage = 'https://www.gnu.org/software/wget' +description = """GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, + the most widely-used Internet protocols. It is a non-interactive commandline tool, + so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + {SOURCE_TAR_GZ: 'fa2dc35bab5184ecbc46a9ef83def2aaaa3f4c9f3c97d4bd19dcb07d4da637de'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('Perl', '5.36.1'), +] +dependencies = [ + ('PCRE', '8.45'), + ('libidn2', '2.3.7'), + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date gnutls for security reasons + # ('GnuTLS', '3.7.1'), +] + +# make sure pkgconfig picks up system packages (OpenSSL & co) +local_pc = "%(sysroot)s/usr/lib64/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig" +preconfigopts = "export PKG_CONFIG_PATH=%s && " % local_pc +configopts = '--with-ssl=openssl ' + +# Optionally, you can use gnutls (default) instead of OpenSSL. +# Do not forget to comment out configopts in that case. +# osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'devel'