diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb index 607e5edebb4..e07ffd64a9e 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb @@ -1345,6 +1345,9 @@ exts_list = [ ('escape', '1.12.0', { 'checksums': ['d69dda267e9346b1d3f10274fb0985409d23060abba609d4e8859eae92b1b12e'], }), + ('plyranges', '1.22.0', { + 'checksums': ['fcdcad1082fadd1a365dd2d2cc7d955601b737ecd4a567d888d2b445756297fc'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} diff --git a/easybuild/easyconfigs/z/zUMIs/zUMIs-2.9.7-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/z/zUMIs/zUMIs-2.9.7-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..3334e3ee95b --- /dev/null +++ b/easybuild/easyconfigs/z/zUMIs/zUMIs-2.9.7-foss-2023a-R-4.3.2.eb @@ -0,0 +1,50 @@ +easyblock = 'Tarball' + +name = 'zUMIs' +version = '2.9.7' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/sdparekh/zUMIs' +description = """A fast and flexible pipeline to process RNA sequencing data with UMIs.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'sdparekh' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['11eb3d99804a67e47b36b69accd0298c93c76b642d801292a618bc7888d34962'] + +dependencies = [ + ('Python', '3.11.3'), + ('pigz', '2.8'), + ('Pysam', '0.22.0'), + ('SAMtools', '1.18'), + ('STAR', '2.7.11a'), + ('R', '4.3.2'), + ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'), +] + +postinstallcmds = [ + # remove updated/deleted/not-working stuff from --help text + "sed -i '33 s/${zumis}/zumis/' %(installdir)s/zUMIs.sh", + "sed -i '43,46d' %(installdir)s/zUMIs.sh", + "sed -i '7,10d' %(installdir)s/zUMIs.sh", + "mkdir -p %(installdir)s/bin", + "ln -s %(installdir)s/zUMIs.sh %(installdir)s/bin/zumis", +] + +modloadmsg = """ +To run zUMIs do not use '$ zUMIs.sh ...' command but only '$ zumis ...' instead. +Do NOT run with conda (do not use flag '-c'). +""" + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': ["bin/zumis"], + 'dirs': [], +} + +sanity_check_commands = ['zumis -h 2>&1 | grep "USAGE"'] + +moduleclass = 'tools'