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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,
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