From c796315c43a2a30ee2a06af4059d3553a044a342 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 28 Oct 2024 17:46:57 +0100 Subject: [PATCH 1/3] adding easyconfigs: tbl2asn-20230713-GCCcore-12.3.0.eb --- .../tbl2asn-20230713-GCCcore-12.3.0.eb | 88 +++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1e03c1f4e24 --- /dev/null +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb @@ -0,0 +1,88 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# revised by Ariel Lozano + +easyblock = 'Bundle' + +name = 'tbl2asn' +version = '20230713' + +homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' +description = """Tbl2asn is a command-line program that automates the creation of + sequence records for submission to GenBank""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +builddependencies = [ + ('binutils', '2.40'), + ('patchelf', '0.18.0'), +] + +# libraries that are copied to installdir need to be patched to have an RPATH section +# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check); + +default_easyblock = 'CmdCp' + +# It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions, +# reporiting the same verion (tbl2asn --help -> 25.8) but 5 out of 6 (gunzipped) executables have different sha256 +# checksums. + +components = [ + ('libidn', '1.34', { + 'easyblock': 'ConfigureMake', + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'start_dir': '%(namelower)s-%(version)s', + 'checksums': ['3719e2975f2fb28605df3479c380af2cf4ab4e919e1506527e4c7670afff6e3c'], + }), + (name, version, { + 'source_urls': ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % + (version[:4] + '-' + version[4:6] + '-' + version[6:])], + 'sources': [{'download_filename': 'tbl2asn.linux64.gz', + 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}], + 'checksums': ['544c4a2a53f2121fd21c44778fc61980a701ce852ea0142979241c0465c38a0c'], + 'cmds_map': [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")], + 'files_to_copy': [(['tbl2asn'], 'bin')], + }), +] + +postinstallcmds = [ + "if %(rpath_enabled)s; then " + " patchelf --force-rpath --set-rpath %(installdir)s/lib %(installdir)s/bin/tbl2asn;" + "fi", + "chmod +x %(installdir)s/bin/tbl2asn", +] + +sanity_check_paths = { + 'files': ['bin/tbl2asn', 'bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ['tbl2asn --help'] + +moduleclass = 'bio' + +# " for lib in $(ls %(installdir)s/lib/libidn.so*); do " +# " echo setting RPATH in $lib;" +# " patchelf --force-rpath --set-rpath %(installdir)s/lib/libidn.so.11 %(installdir)s/bin/tbl2asn" +# " done;" +# +# + +""" + " for lib in $(ls %(installdir)s/lib/libidn.so*); do " + " patchelf --force-rpath --set-rpath '$ORIGIN' $lib;" + " done;" + "fi", + + "if %(rpath_enabled)s; then " + " for lib in $(ls %(installdir)s/lib/libidn.so*); do " + " patchelf --force-rpath --set-rpath %(installdir)s/bin/tbl2asn $lib;" + " done;" + "fi", + + "if %(rpath_enabled)s; then " + " patchelf --force-rpath --set-rpath '$ORIGIN' %(installdir)s/lib/libidn.so.11;" + "fi", +""" \ No newline at end of file From 206e1526e91256577afbf6a661b8e2e9dfee3f69 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 28 Oct 2024 17:50:53 +0100 Subject: [PATCH 2/3] clean up config --- .../tbl2asn-20230713-GCCcore-12.3.0.eb | 26 +------------------ 1 file changed, 1 insertion(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb index 1e03c1f4e24..68563984e25 100644 --- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb @@ -61,28 +61,4 @@ sanity_check_paths = { sanity_check_commands = ['tbl2asn --help'] -moduleclass = 'bio' - -# " for lib in $(ls %(installdir)s/lib/libidn.so*); do " -# " echo setting RPATH in $lib;" -# " patchelf --force-rpath --set-rpath %(installdir)s/lib/libidn.so.11 %(installdir)s/bin/tbl2asn" -# " done;" -# -# - -""" - " for lib in $(ls %(installdir)s/lib/libidn.so*); do " - " patchelf --force-rpath --set-rpath '$ORIGIN' $lib;" - " done;" - "fi", - - "if %(rpath_enabled)s; then " - " for lib in $(ls %(installdir)s/lib/libidn.so*); do " - " patchelf --force-rpath --set-rpath %(installdir)s/bin/tbl2asn $lib;" - " done;" - "fi", - - "if %(rpath_enabled)s; then " - " patchelf --force-rpath --set-rpath '$ORIGIN' %(installdir)s/lib/libidn.so.11;" - "fi", -""" \ No newline at end of file +moduleclass = 'bio' \ No newline at end of file From 8bf310cc1a2901cebd5ddfd308dfc3626c375929 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 28 Oct 2024 18:19:49 +0100 Subject: [PATCH 3/3] add blank line to end of file --- .../easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb index 68563984e25..dcf4c39e8d0 100644 --- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb @@ -61,4 +61,4 @@ sanity_check_paths = { sanity_check_commands = ['tbl2asn --help'] -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio'