From 930f4bc8e90315ef2034e6ac2b873739a1135413 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 28 Jan 2025 15:56:21 +0100
Subject: [PATCH 1/2] adding easyconfigs: UFCG-1.0.6-foss-2023a.eb

---
 .../u/UFCG/UFCG-1.0.6-foss-2023a.eb           | 40 +++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 easybuild/easyconfigs/u/UFCG/UFCG-1.0.6-foss-2023a.eb

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..953a63afdf3
--- /dev/null
+++ b/easybuild/easyconfigs/u/UFCG/UFCG-1.0.6-foss-2023a.eb
@@ -0,0 +1,40 @@
+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}]
+checksums = ['6641dd636c7f13f3e754163a50e3eda9e1d9b0ebad8eaa42422acaa410210bc7']
+
+builddependencies = [
+    ('Maven', '3.9.7', '', SYSTEM),
+]
+dependencies = [
+    ('Java', '21', '', 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',
+]
+
+sanity_check_paths = {
+    'files': ['%(namelower)s-%(version)s.jar', 'bin/%(namelower)s'],
+    'dirs': ['bin', 'repo', 'classes'],
+}
+sanity_check_commands = ['%(namelower)s -h']
+
+moduleclass = 'bio'

From ff082d7011b62563569c3ab6e044eb2e3e45834e Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 28 Jan 2025 19:18:48 +0100
Subject: [PATCH 2/2] fix ping + init download

---
 .../easyconfigs/u/UFCG/UFCG-1.0.6-foss-2023a.eb   |  9 +++++++--
 .../easyconfigs/u/UFCG/UFCG-1.0.6_fix-ping.patch  | 15 +++++++++++++++
 2 files changed, 22 insertions(+), 2 deletions(-)
 create mode 100644 easybuild/easyconfigs/u/UFCG/UFCG-1.0.6_fix-ping.patch

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
index 953a63afdf3..aae8aaceeea 100644
--- a/easybuild/easyconfigs/u/UFCG/UFCG-1.0.6-foss-2023a.eb
+++ b/easybuild/easyconfigs/u/UFCG/UFCG-1.0.6-foss-2023a.eb
@@ -11,13 +11,17 @@ 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}]
-checksums = ['6641dd636c7f13f3e754163a50e3eda9e1d9b0ebad8eaa42422acaa410210bc7']
+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', '21', '', SYSTEM),
+    ('Java', '11', '', SYSTEM),
     ('AUGUSTUS', '3.5.0'),
     ('MMseqs2', '14-7e284'),
     ('MAFFT', '7.520', '-with-extensions'),
@@ -29,6 +33,7 @@ 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 = {
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'));