diff --git a/easybuild/easyconfigs/u/UFCG/UFCG-1.0.6-foss-2023a.eb b/easybuild/easyconfigs/u/UFCG/UFCG-1.0.6-foss-2023a.eb new file mode 100644 index 00000000000..aae8aaceeea --- /dev/null +++ b/easybuild/easyconfigs/u/UFCG/UFCG-1.0.6-foss-2023a.eb @@ -0,0 +1,45 @@ +easyblock = 'Binary' + +name = 'UFCG' +version = '1.0.6' + +homepage = 'https://github.com/steineggerlab/ufcg/' +description = """UFCG pipeline provides methods for a genome-wide taxonomic profiling +and annotation of your own biological sequences of Fungi.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/steineggerlab/ufcg/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['%(name)s-%(version)s_fix-ping.patch'] +checksums = [ + {'UFCG-1.0.6.tar.gz': '6641dd636c7f13f3e754163a50e3eda9e1d9b0ebad8eaa42422acaa410210bc7'}, + {'UFCG-1.0.6_fix-ping.patch': 'd5419a8fdbf8177f39b0fb4888418cb7261b3a758f7164fdc2252e96d5aea307'}, +] + +builddependencies = [ + ('Maven', '3.9.7', '', SYSTEM), +] +dependencies = [ + ('Java', '11', '', SYSTEM), + ('AUGUSTUS', '3.5.0'), + ('MMseqs2', '14-7e284'), + ('MAFFT', '7.520', '-with-extensions'), + ('IQ-TREE', '2.3.5'), +] + +extract_sources = True + +install_cmds = [ + 'mvn clean package appassembler:assemble', + 'cp -r %(start_dir)s/target/* %(installdir)s', + '%(installdir)s/bin/ufcg download -t minimum', +] + +sanity_check_paths = { + 'files': ['%(namelower)s-%(version)s.jar', 'bin/%(namelower)s'], + 'dirs': ['bin', 'repo', 'classes'], +} +sanity_check_commands = ['%(namelower)s -h'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/u/UFCG/UFCG-1.0.6_fix-ping.patch b/easybuild/easyconfigs/u/UFCG/UFCG-1.0.6_fix-ping.patch new file mode 100644 index 00000000000..b3a1583e5dc --- /dev/null +++ b/easybuild/easyconfigs/u/UFCG/UFCG-1.0.6_fix-ping.patch @@ -0,0 +1,15 @@ +Fix function internetConnection to prevent run ping and internet connection error. +https://github.com/steineggerlab/ufcg/blob/cf9cfe3c2950c8d17447864da4574014db5a90f7/src/module/DownloadModule.java#L121 +--- src/module/DownloadModule.java.orig 2025-01-28 18:06:36.553823000 +0100 ++++ src/module/DownloadModule.java 2025-01-28 18:28:36.023487000 +0100 +@@ -119,9 +119,7 @@ + } + + private boolean internetConnection(){ +- String[] raw = Shell.exec(String.format("ping -c 1 -W %d ufcg.steineggerlab.workers.dev", GenericConfig.OS.equals("Linux") ? 1 : 1000), true, 0); +- if(raw == null || raw.length < 2) return false; +- return raw[raw.length - 2].contains(GenericConfig.OS.equals("Linux") ? "1 received" : "1 packets received"); ++ return true; + } + private void printManual() { + System.out.println(ANSIHandler.wrapper(" UFCG - download", 'G'));