From cc1896e63631b96c608580d51486c5927f7b3517 Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Wed, 7 Feb 2024 14:31:50 +0000
Subject: [PATCH] remove unused custom easyblock for SNPhylo (`snphylo.py`)

---
 easybuild/easyblocks/s/snphylo.py | 104 ------------------------------
 1 file changed, 104 deletions(-)
 delete mode 100644 easybuild/easyblocks/s/snphylo.py

diff --git a/easybuild/easyblocks/s/snphylo.py b/easybuild/easyblocks/s/snphylo.py
deleted file mode 100644
index 7fed0ace86..0000000000
--- a/easybuild/easyblocks/s/snphylo.py
+++ /dev/null
@@ -1,104 +0,0 @@
-##
-# Copyright 2009-2023 Ghent University
-#
-# This file is part of EasyBuild,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
-# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# https://github.com/easybuilders/easybuild
-#
-# EasyBuild is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation v2.
-#
-# EasyBuild is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
-##
-"""
-EasyBuild support for SNPyhlo, implemented as an easyblock
-
-@authors: Ewan Higgs (HPC-UGent)
-@authors: Kenneth Hoste (HPC-UGent)
-"""
-import os
-import re
-import stat
-from easybuild.tools import LooseVersion
-
-from easybuild.framework.easyblock import EasyBlock
-from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.filetools import adjust_permissions, copy_dir, copy_file, mkdir
-from easybuild.tools.modules import get_software_root, get_software_version
-from easybuild.tools.run import run_cmd
-
-
-class EB_SNPhylo(EasyBlock):
-    """Support for building and installing SNPhylo."""
-
-    def __init__(self, *args, **kwargs):
-        """Set custom class variables."""
-        super(EB_SNPhylo, self).__init__(*args, **kwargs)
-
-        self.scripts_path = os.path.join('bin', 'scripts')
-
-    def configure_step(self):
-        """No configure step for SNPhylo."""
-        pass
-
-    def build_step(self):
-        """No build step for SNPhylo."""
-
-        # check for required dependencies
-        for dep in ['MUSCLE', 'PHYLIP', 'Python', 'R']:
-            if not get_software_root(dep):
-                raise EasyBuildError("Required dependency '%s' not loaded", dep)
-
-        # check for required R libraries
-        rver = get_software_version('R')
-        r_libs, _ = run_cmd("R --vanilla --no-save --slave -e 'print(installed.packages())'", simple=False)
-        for rpkg in ['gdsfmt', 'getopt', 'SNPRelate', 'phangorn']:
-            if not re.search(r'^%s\s.*%s' % (rpkg, rver), r_libs, re.M):
-                raise EasyBuildError("Required R package '%s' not installed", rpkg)
-
-        # run setup.sh, and send a bunch of newlines as stdin to 'answer' the Q&A;
-        # all questions can be answered with the default answer (if the dependencies are specified correctly);
-        # use run_cmd_qa doesn not work because of buffering issues (questions are not coming through)
-        adjust_permissions('setup.sh', stat.S_IXUSR, add=True)
-        (out, _) = run_cmd('bash ./setup.sh', inp='\n' * 10, simple=False)
-
-        success_msg = "SNPHYLO is successfully installed!!!"
-        if success_msg not in out:
-            raise EasyBuildError("Success message '%s' not found in setup.sh output: %s", success_msg, out)
-
-    def install_step(self):
-        """Install by copying files/directories."""
-        bindir = os.path.join(self.installdir, 'bin')
-        binfiles = ['snphylo.sh', 'snphylo.cfg', 'snphylo.template']
-
-        # Starting from v20160204 the source archive has a different directory tree
-        if LooseVersion(self.version) >= LooseVersion('20160204'):
-            predir = 'SNPhylo'
-        else:
-            predir = ''
-
-        mkdir(bindir, parents=True)
-        for binfile in binfiles:
-            copy_file(os.path.join(self.builddir, predir, binfile), bindir)
-
-        copy_dir(os.path.join(self.builddir, predir, 'scripts'), os.path.join(self.installdir, self.scripts_path))
-
-    def sanity_check_step(self):
-        """Custom sanity check for SNPhylo."""
-        custom_paths = {
-            'files': ['bin/snphylo.sh', 'bin/snphylo.cfg', 'bin/snphylo.template'],
-            'dirs': [self.scripts_path],
-        }
-        super(EB_SNPhylo, self).sanity_check_step(custom_paths=custom_paths)