diff --git a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb index 734e544fc9f..f62a0b1e28b 100644 --- a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb @@ -41,8 +41,7 @@ sanity_check_paths = { 'dirs': [], } -modextravars = { - "LC_ALL": "en_US.UTF-8", -} +# required to work around localization bug, see https://github.com/mozack/abra2/issues/25 +modextravars = {'LC_ALL': 'en_US.UTF-8'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb index fdf461c95d4..e4693c5f0e3 100644 --- a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb @@ -9,17 +9,15 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/pinetree1/crispr-dav/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['crispr-dav-2.3.4_remove_hardcoding.patch'] +patches = ['CRISPR-DAV-%(version)s_remove_hardcoding.patch'] checksums = [ '49975cd48bdbf31fe5a9e2aaa3f5ed85d3cc6f65a422ee3aa8daed890159d2ae', # v2.3.4.tar.gz # crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch '41475a09754d65cc2c88d4161be6eacdfc98242bccbe49778c4f1f74210a6cb2', ] -# also needs `naturalsort`, which is now an R extension - see https://github.com/easybuilders/easybuild-easyconfigs/pull/13762 -# if missing, try reinstalling R (https://docs.easybuild.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-skip) dependencies = [ - ('R', '4.0.3'), + ('R', '4.0.3'), # provides naturalsort R package ('Perl', '5.32.0'), ('NGS', '2.10.9'), ('Pysam', '0.16.0.1'), diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/crispr-dav-2.3.4_remove_hardcoding.patch b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4_remove_hardcoding.patch similarity index 100% rename from easybuild/easyconfigs/c/CRISPR-DAV/crispr-dav-2.3.4_remove_hardcoding.patch rename to easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4_remove_hardcoding.patch diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb index c7576441aed..c2fccb2c6a2 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb @@ -77,23 +77,21 @@ exts_list = [ }), ] -# this is the script which relies in many extra Perl libraries so we verify it's working fine -sanity_check_commands = ['%(installdir)s/prinseq-graphs.pl'] +fix_perl_shebang_for = ["*.pl"] -modextrapaths = { - 'PATH': '', - 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', -} +postinstallcmds = ["chmod +x %(installdir)s/*.pl"] -postinstallcmds = [ - "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", - "chmod +x %(installdir)s/*.pl", -] +# this is the script which relies in many extra Perl libraries so we verify it's working fine +sanity_check_commands = ['%(installdir)s/prinseq-graphs.pl'] sanity_check_paths = { 'files': ['prinseq-lite.pl', 'prinseq-graphs.pl', 'prinseq-graphs-noPCA.pl'], 'dirs': [] } +modextrapaths = { + 'PATH': '', + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} moduleclass = 'bio'