diff options
Diffstat (limited to 'quast.patch')
| -rw-r--r-- | quast.patch | 88 |
1 files changed, 88 insertions, 0 deletions
diff --git a/quast.patch b/quast.patch new file mode 100644 index 0000000..31e5460 --- /dev/null +++ b/quast.patch @@ -0,0 +1,88 @@ +This patch is mostly adapted from the Debian patches +https://salsa.debian.org/med-team/quast/-/tree/master/debian/patches + +diff --git a/setup.py b/setup.py +index a982a430..24ab2f5f 100755 +--- a/setup.py ++++ b/setup.py +@@ -35,10 +35,10 @@ except: + exit_with_code=1) + + from quast_libs.glimmer import compile_glimmer +-from quast_libs.run_busco import download_augustus, download_all_db +-from quast_libs.search_references_meta import download_blast_binaries, download_blastdb ++from quast_libs.run_busco import download_all_db ++from quast_libs.search_references_meta import download_blastdb + from quast_libs.ca_utils.misc import compile_aligner +-from quast_libs.ra_utils.misc import compile_reads_analyzer_tools, compile_bwa, compile_bedtools, download_gridss ++from quast_libs.ra_utils.misc import compile_reads_analyzer_tools, download_gridss + + name = 'quast' + quast_package = qconfig.PACKAGE_NAME +@@ -60,8 +60,6 @@ if cmd_in(['clean', 'sdist']): + logger.info('Cleaning up binary files...') + compile_aligner(logger, only_clean=True) + compile_glimmer(logger, only_clean=True) +- compile_bwa(logger, only_clean=True) +- compile_bedtools(logger, only_clean=True) + for fpath in [fn for fn in glob(join(quast_package, '*.pyc'))]: os.remove(fpath) + for fpath in [fn for fn in glob(join(quast_package, 'html_saver', '*.pyc'))]: os.remove(fpath) + for fpath in [fn for fn in glob(join(quast_package, 'site_packages', '*', '*.pyc'))]: os.remove(fpath) +@@ -74,10 +72,7 @@ if cmd_in(['clean', 'sdist']): + if isdir(name + '.egg-info'): + shutil.rmtree(name + '.egg-info') + download_gridss(logger, only_clean=True) +- download_blast_binaries(logger, only_clean=True) +- download_blastdb(logger, only_clean=True) + if qconfig.platform_name != 'macosx': +- download_augustus(logger, only_clean=True) + download_all_db(logger, only_clean=True) + logger.info('Done.') + sys.exit() +@@ -168,9 +163,6 @@ if cmd_in(['install', 'develop', 'build', 'build_ext']): + logger.info('* Downloading GRIDSS *') + if not download_gridss(logger): + modules_failed_to_install.append('GRIDSS (affects -1/--reads1 and -2/--reads2 options)') +- logger.info('* Downloading BLAST *') +- if not download_blast_binaries(logger): +- modules_failed_to_install.append('BLAST (affects metaquast.py in without references mode and --find-conserved-genes option)') + logger.info('* Downloading SILVA 16S rRNA gene database *') + if not download_blastdb(logger): + modules_failed_to_install.append('SILVA 16S rRNA gene database (affects metaquast.py in without references mode)') +@@ -186,20 +178,8 @@ if cmd_in(['install', 'develop', 'build', 'build_ext']): + logger.info('') + + +-if qconfig.platform_name == 'macosx': +- sambamba_files = [join('sambamba', 'sambamba_osx')] +-else: +- sambamba_files = [join('sambamba', 'sambamba_linux')] +- +-minimap_files = find_package_files('minimap2') +-bwa_files = [ +- join('bwa', fp) for fp in os.listdir(join(quast_package, 'bwa')) +- if isfile(join(quast_package, 'bwa', fp)) and fp.startswith('bwa')] +-bedtools_files = [join('bedtools', 'bin', '*')] + full_install_tools = ( +- find_package_files('gridss') + +- find_package_files('blast') + +- [join(quast_package, 'busco', 'hmmsearch')] ++ find_package_files('gridss') + ) + + setup( +@@ -229,14 +209,10 @@ The tool accepts multiple assemblies, thus is suitable for comparison.''', + 'manual.html', + ] + + find_package_files('html_saver') + +- minimap_files + + find_package_files('genemark/' + qconfig.platform_name) + + find_package_files('genemark-es/' + qconfig.platform_name) + + find_package_files('genemark-es/lib') + + find_package_files('glimmer') + +- bwa_files + +- bedtools_files + +- sambamba_files + + (full_install_tools if install_full else []) + }, + include_package_data=True, |