diff options
Diffstat (limited to 'gn/packages/patches/quast.patch')
| -rw-r--r-- | gn/packages/patches/quast.patch | 88 |
1 files changed, 0 insertions, 88 deletions
diff --git a/gn/packages/patches/quast.patch b/gn/packages/patches/quast.patch deleted file mode 100644 index 31e5460..0000000 --- a/gn/packages/patches/quast.patch +++ /dev/null @@ -1,88 +0,0 @@ -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, |