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,