Merge pull request easybuilders#19811 from PetrKralCZ/20240208100552_…

…new_pr_MSFragger40

{bio}[system/system] MSFragger v4.0 w/ Java 11

easybuild/easyconfigs/m/MSFragger/MSFragger-4.0-Java-11.eb

@@ -0,0 +1,39 @@
+easyblock = 'Tarball'
+
+name = 'MSFragger'
+version = '4.0'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://msfragger.nesvilab.org/'
+description = """MSFragger is an ultrafast database search tool for peptide identification
+ in mass spectrometry-based proteomics. It has demonstrated excellent performance across a wide
+ range of datasets and applications. MSFragger is suitable for standard shotgun proteomics
+ analyses as well as large datasets (including timsTOF PASEF data), enzyme unconstrained
+ searches (e.g., peptidome), open database searches (e.g., precursor mass tolerance set
+ to hundreds of Daltons) for identification of modified peptides, and glycopeptide
+ identification (N-linked and O-linked)."""
+
+toolchain = SYSTEM
+
+sources = ['%(name)s-%(version)s.zip']
+checksums = ['25bdab705c4ac97729d1da8d7a075e3920d8a447596fa52eff8e564606d1720e']
+
+download_instructions = 'Manual download required, see http://msfragger-upgrader.nesvilab.org/upgrader/'
+
+dependencies = [('Java', '11')]
+
+postinstallcmds = [
+    "mkdir -p %(installdir)s/bin",
+    "echo '#!/bin/sh' > %(installdir)s/bin/%(namelower)s",
+    "echo 'java -jar %(installdir)s/%(name)s-%(version)s.jar $@' >> %(installdir)s/bin/%(namelower)s",
+    "chmod a+rx %(installdir)s/bin/%(namelower)s",
+]
+
+sanity_check_paths = {
+    'files': ['%(name)s-%(version)s.jar'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['%(namelower)s --help']
+
+moduleclass = 'bio'