add custom easyblock for CRISPR-DAV

easybuild/easyblocks/c/crispr_dav.py

@@ -0,0 +1,168 @@
+##
+# Copyright 2020-2021 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 CRISPR-DAV, implemented as an easyblock.
+
+@author: Denis Kristak (INUITS)
+@author: Kenneth Hoste (HPC-UGent)
+"""
+import glob
+import os
+from easybuild.easyblocks.generic.binary import Binary
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import apply_regex_substitutions, back_up_file, write_file
+from easybuild.tools.modules import get_software_root
+
+
+class EB_CRISPR_minus_DAV(Binary):
+    """
+    Support for building/installing CRISPR-DAV.
+    """
+
+    def __init__(self, *args, **kwargs):
+        """Constructor for CRISPR-DAV easyblock."""
+        super(EB_CRISPR_minus_DAV, self).__init__(*args, **kwargs)
+        self.cfg['extract_sources'] = True
+
+    def post_install_step(self):
+        """Update configuration files with correct paths to dependencies and files in installation."""
+
+        # getting paths of deps + files we will work with
+        example_dir = os.path.join(self.installdir, 'Examples')
+        config_file = os.path.join(self.installdir, 'conf.txt')
+
+        dep_roots = {}
+        for dep in ('ABRA2', 'BEDTools', 'FLASH', 'Java', 'PRINSEQ', 'pysamstats', 'R', 'SAMtools'):
+            root = get_software_root(dep)
+            if root:
+                dep_roots[dep] = root
+            else:
+                raise EasyBuildError("Failed to find root directory for %s. Is it included as dependency?", dep)
+
+        # we will be changing both Examples/... conf file (for sanity checks) as well as root (for proper functioning)
+        cfg_files = [config_file] + glob.glob(os.path.join(example_dir, 'example*', 'conf.txt'))
+
+        # create a backup of original Examples/example1/conf.txt file + the root conf.txt file
+        for filename in cfg_files:
+            back_up_file(filename)
+
+        # according to docs, we have to setup conf.txt so that it contains correct paths to dependencies
+        # https://github.com/pinetree1/crispr-dav/blob/master/Install-and-Run.md
+        # User then has to change conf.txt to include paths to genomes
+        # changing both example conf.txt as well as the main one (in root directory) to make it easier for user.
+
+        # func to replace everything in both conf.txt files
+        self.modify_conf_files(dep_roots, cfg_files)
+
+        # generating fastq file with correct paths (used for sanity checks)
+        for example in ('example1', 'example2'):
+            example_dir = os.path.join(example_dir, example)
+            fastq_list_file = os.path.join(example_dir, 'fastq.list')
+            fastq_list = []
+            rawfastq_dir = os.path.join(example_dir, 'rawfastq')
+
+            for x in range(1, 5):
+                # we have to use \t or it wont work!
+                line = '\t'.join([
+                    'sample%s' % x,
+                    os.path.join(rawfastq_dir, 'sample%s_R1.fastq.gz' % x),
+                    os.path.join(rawfastq_dir, 'sample%s_R2.fastq.gz' % x),
+                ])
+                fastq_list.append(line)
+
+            # last line should not end with newline (\n)!
+            write_file(fastq_list_file, '\n'.join(fastq_list))
+
+    def sanity_check_step(self):
+        """Custom sanity check paths for CRISPR-DAV"""
+        custom_paths = {
+            'files': ['crispr.pl'],
+            'dirs': ['Modules', 'Examples', 'Rscripts'],
+        }
+
+        # example command from docs - https://github.com/pinetree1/crispr-dav/blob/master/Install-and-Run.md
+        # this command is an improvement (no hardcoded stuff) of
+        # https://github.com/pinetree1/crispr-dav/blob/master/Examples/example1/run.sh
+        example_dir = os.path.join(self.installdir, 'Examples', 'example1')
+        outfile = os.path.join(self.builddir, 'test.out')
+        example_cmd = ' '.join([
+            os.path.join(self.installdir, 'crispr.pl'),
+            "--conf %s" % os.path.join(example_dir, 'conf.txt'),
+            "--region %s" % os.path.join(example_dir, 'amplicon.bed'),
+            "--crispr %s" % os.path.join(example_dir, 'site.bed'),
+            "--sitemap %s" % os.path.join(example_dir, 'sample.site'),
+            "--fastqmap %s" % os.path.join(example_dir, 'fastq.list'),
+            "--conf %s" % os.path.join(example_dir, 'conf.txt'),
+            "--genome genomex",
+            "2>&1 | tee %s" % outfile,
+            " && grep 'Generated HTML report for GENEX_CR1' %s" % outfile,
+        ])
+
+        custom_commands = [
+            "crispr.pl --help 2>&1 | grep 'Usage: '",
+            example_cmd,
+        ]
+
+        super(EB_CRISPR_minus_DAV, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)
+
+    def make_module_extra(self):
+        txt = super(EB_CRISPR_minus_DAV, self).make_module_extra()
+        txt += self.module_generator.prepend_paths('PATH', [''])
+        return txt
+
+    def modify_conf_files(self, dep_roots, cfg_files):
+        """Replace hardcoded paths in config files."""
+
+        abra2_jar = os.path.join(dep_roots['ABRA2'], 'abra2-%s.jar' % os.getenv('EBVERSIONABRA2'))
+        pysamstats_bin = os.path.join(dep_roots['pysamstats'], 'bin', 'pysamstats')
+
+        regex_subs = [
+            (r'^abra\s*=.*/abra.*.jar', 'abra = ' + abra2_jar),
+            (r'^bedtools\s*=.*/bin/bedtools', 'bedtools = ' + os.path.join(dep_roots['BEDTools'], 'bin', 'bedtools')),
+            (r'^flash\s*=.*/bin/flash2', 'flash = ' + os.path.join(dep_roots['FLASH'], 'bin', 'flash2')),
+            (r'^java\s*=.*/bin/java', 'java = ' + os.path.join(dep_roots['Java'], 'bin', 'java')),
+            (r'^prinseq\s*=.*/prinseq-lite.pl', 'prinseq = ' + os.path.join(dep_roots['PRINSEQ'], 'prinseq-lite.pl')),
+            (r'^pysamstats\s*=.*/bin/pysamstats', 'pysamstats = ' + pysamstats_bin),
+            (r'^rscript\s*=.*/bin/Rscript', 'rscript = ' + os.path.join(dep_roots['R'], 'bin', 'Rscript')),
+            (r'^samtools\s*=.*/bin/samtools', 'samtools = ' + os.path.join(dep_roots['SAMtools'], 'bin', 'samtools')),
+        ]
+
+        for cfg_file in cfg_files:
+            dirname = os.path.dirname(cfg_file)
+            if os.path.basename(dirname).startswith('example'):
+                example_dir = dirname
+            else:
+                example_dir = os.path.join(self.installdir, 'Examples', 'example1')
+
+            genome_dir = os.path.join(example_dir, 'genome')
+            genomex_fa = os.path.join(genome_dir, 'genomex.fa')
+
+            regex_subs.extend([
+                (r'^ref_fasta\s*=.*genome/genomex.fa', 'ref_fasta = ' + genomex_fa),
+                (r'^bwa_idx\s*=.*genome/genomex.fa', 'bwa_idx = ' + genomex_fa),
+                (r'^refGene\s*=.*genome/refgenex.txt', 'refGene = ' + os.path.join(genome_dir, 'refgenex.txt')),
+            ])
+
+            apply_regex_substitutions(cfg_file, regex_subs, on_missing_match='error')