new easyblock for RepeatModeler

easybuild/easyblocks/r/repeatmodeler.py

@@ -0,0 +1,196 @@
+##
+# Copyright 2009-2021 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 building and installing RepeatModeler, implemented as an easyblock
+
+@author: Jasper Grimm (UoY)
+"""
+
+import os
+
+from easybuild.easyblocks.generic.tarball import Tarball
+from easybuild.easyblocks.perl import get_site_suffix
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import change_dir, patch_perl_script_autoflush
+from easybuild.tools.modules import get_software_root
+from easybuild.tools.run import run_cmd_qa
+
+
+def get_dep_path(dep_name, rel_path, log, optional):
+    """
+    Check for dependency, raise error if it's not available (unless optional=True is used).
+    Return full path to specified relative path in dependency installation directory,
+    return None if optional dependency is not found.
+    """
+
+    dep_root = get_software_root(dep_name)
+    if dep_root:
+        dep = os.path.join(dep_root, rel_path)
+        return dep
+    elif optional:
+        log.info("Optional dependency not found: %s" % dep_name)
+        return ''
+    else:
+        raise EasyBuildError("Missing required dependency: %s" % dep_name)
+
+
+class EB_RepeatModeler(Tarball):
+    """Support for building/installing RepeatModeler."""
+
+    def install_step(self):
+        """Custom install procedure for RepeatModeler."""
+        super(EB_RepeatModeler, self).install_step()
+
+        # Required dependencies, and bin path relative to software root
+        required_deps = {
+            'CD-HIT': 'bin',
+            'Kent_tools': 'bin',
+            'Perl': os.path.join('bin', 'perl'),
+            'RECON': 'bin',
+            'RepeatMasker': '',
+            'RepeatScout': '',
+            'TRF': os.path.join('bin', 'trf'),
+        }
+
+        # Search engines, and bin path relative to software root
+        search_engines = {
+            'ABBlast': 'bin',
+            'RMBlast': 'bin',
+            'WUBlast': 'bin',
+        }
+
+        # Optional dependencies for LTR pipeline, and bin path relative to software root
+        optional_LTR_deps = {
+            'GenomeTools': 'bin',
+            'LTR_retriever': '',
+            'MAFFT': 'bin',
+            'TWL-NINJA': 'bin',
+        }
+
+        for dep, path in required_deps.items():
+            required_deps[dep] = get_dep_path(dep, path, log=self.log, optional=False)
+
+        for dep, path in search_engines.items():
+            search_engines[dep] = get_dep_path(dep, path, log=self.log, optional=True)
+
+        for dep, path in optional_LTR_deps.items():
+            optional_LTR_deps[dep] = get_dep_path(dep, path, log=self.log, optional=True)
+
+        # Check at least one search engine is present, and not both ABBlast/WUBlast
+        if not any(search_engines.values()):
+            raise EasyBuildError("At least one search engine must be specified: RMBlast, ABBlast, WUBlast")
+        elif search_engines['ABBlast'] and search_engines['WUBlast']:
+            raise EasyBuildError("Cannot specify both ABBlast and WUBlast")
+
+        # Check if all LTR Pipeline dependencies present
+        if all(optional_LTR_deps.values()):
+            self.log.info("All LTR pipeline dependencies found, enabling LTR support")
+            with_LTR = 'y'
+        else:
+            self.log.info("Not all LTR pipeline dependencies found, disabling LTR support")
+            with_LTR = 'n'
+
+        # Map search engine to configuration option
+        search_engine_map = {
+            'ABBlast': '2',
+            'RMBlast': '1',
+            'WUBlast': '2',
+        }
+
+        # List of search engines to use (mapped)
+        mapped_engines = [search_engine_map[k] for k, v in search_engines.items() if v] + ['3']
+
+        change_dir(self.installdir)
+
+        # Fix perl shebang in configure script (#!/usr/local/bin/perl)
+        orig_fix_perl_shebang_for = self.cfg['fix_perl_shebang_for']
+        self.cfg['fix_perl_shebang_for'] = [os.path.join(self.installdir, 'configure')]
+        self.fix_shebang()
+        self.cfg['fix_perl_shebang_for'] = orig_fix_perl_shebang_for
+
+        patch_perl_script_autoflush('configure')
+
+        qa = {
+            '<PRESS ENTER TO CONTINUE>': '',
+        }
+        std_qa = {
+            r'\*\*PERL INSTALLATION PATH\*\*\n\n[^*]*\n+Enter path.*:\s*': required_deps['Perl'],
+            r'UCSCTOOLS_DIR.*:\s*': required_deps['Kent_tools'],
+            r'LTR_RETRIEVER_DIR.*:\s*': optional_LTR_deps['LTR_retriever'],
+            r'RMBLAST_DIR.*:\s*': search_engines['RMBlast'],
+            r'ABBLAST_DIR.*:\s*': search_engines['ABBlast'] or search_engines['WUBlast'],
+            # Configure first engine
+            r'.*(\[ Un\-configured \]\n.*){2}\n.*\n+Enter Selection\:\s*': mapped_engines[0],
+            # Configure second engine if multiple specified, otherwise skip
+            r'.*(\[ Un\-configured \]\n.*\[ Configured \]|\[ Configured \]\n.*\[ Un-configured \])'
+            r'\n\n.*\n+Enter Selection\:\s*': mapped_engines[1],
+            # All engines configured
+            r'.*(\[ Configured \]\n.*){2}\n.*\n+Enter Selection\:\s*': '3',
+            # LTR
+            r'LTR.*\[optional](.*\n)*of analysis \[y] or n\?\:\s*': with_LTR,
+        }
+
+        cmdopts = ' ' + ' '.join([
+            '-trf_prgm "%(TRF)s"',
+            '-repeatmasker_dir "%(RepeatMasker)s"',
+            '-rscout_dir "%(RepeatScout)s"',
+            '-recon_dir "%(RECON)s"',
+            '-ucsctools_dir "%(Kent_tools)s"',
+            '-cdhit_dir "%(CD-HIT)s"',
+        ]) % required_deps
+
+        if with_LTR:
+            cmdopts += ' ' + ' '.join([
+                '-mafft_dir "%(MAFFT)s"',
+                '-genometools_dir "%(GenomeTools)s"',
+                '-ltr_retriever_dir "%(LTR_retriever)s"',
+                '-ninja_dir "%(TWL-NINJA)s"',
+            ]) % optional_LTR_deps
+
+        cmd = "perl ./configure" + cmdopts
+        run_cmd_qa(cmd, qa, std_qa=std_qa, log_all=True, simple=True, log_ok=True, maxhits=100)
+
+    def sanity_check_step(self):
+        """Custom sanity check for RepeatModeler."""
+
+        custom_paths = {
+            'files': ['BuildDatabase', 'RepeatClassifier', 'RepeatModeler', 'RepeatUtil.pm'],
+            'dirs': ['Libraries', 'Matrices', 'util'],
+        }
+
+        custom_commands = [("RepeatModeler -help 2>&1 | grep 'RepeatModeler - Model repetitive DNA'", '')]
+
+        super(EB_RepeatModeler, self).sanity_check_step(custom_commands=custom_commands, custom_paths=custom_paths)
+
+    def make_module_req_guess(self):
+        """Custom guesses for path-like environment variables for RepeatModelerConfig."""
+        guesses = super(EB_RepeatModeler, self).make_module_req_guess()
+
+        guesses.update({
+            'PATH': [''],
+            'PERL5LIB': [get_site_suffix('sitelib')],
+        })
+
+        return guesses