Andreas Tille pushed to branch master at Debian Med / quast
Commits: 55e0dd6a by Andreas Tille at 2020-06-26T13:37:49+02:00 Test suite is now running - - - - - 3 changed files: - − debian/TODO - debian/control - debian/patches/noBwa.patch Changes: ===================================== debian/TODO deleted ===================================== @@ -1,51 +0,0 @@ -moeller@steffen-laptop-debian:~/git/med-team/quast$ PATH=$PATH:. ./setup.py test -./quast.py --test - -Version: 5.0.2, eb9b333 - -System information: - OS: Linux-5.6.0-2-amd64-x86_64-with-glibc2.29 (linux_64) - Python version: 3.8.3 - CPUs number: 2 - -Started: 2020-06-24 17:39:08 - -Logging to /home/moeller/git/med-team/quast/quast_test_output/quast.log -NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually) - -CWD: /home/moeller/git/med-team/quast -Main parameters: - MODE: default, threads: 1, minimum contig length: 500, minimum alignment length: 65, \ - ambiguity: one, threshold for extensive misassembly size: 1000 - -Reference: - /home/moeller/git/med-team/quast/test_data/reference.fasta.gz ==> reference - -Contigs: - Pre-processing... - 1 /home/moeller/git/med-team/quast/test_data/contigs_1.fasta ==> contigs_1 - 2 /home/moeller/git/med-team/quast/test_data/contigs_2.fasta ==> contigs_2 - -module 'cgi' has no attribute 'escape' -Traceback (most recent call last): - File "./quast.py", line 307, in <module> - return_code = main(sys.argv[1:]) - File "./quast.py", line 148, in main - from quast_libs import basic_stats - File "/home/moeller/git/med-team/quast/quast_libs/basic_stats.py", line 15, in <module> - from quast_libs.circos import set_window_size - File "/home/moeller/git/med-team/quast/quast_libs/circos.py", line 25, in <module> - from quast_libs.icarus_utils import get_assemblies, check_misassembled_blocks, Alignment - File "/home/moeller/git/med-team/quast/quast_libs/icarus_utils.py", line 15, in <module> - from quast_libs.html_saver.html_saver import trim_ref_name - File "/home/moeller/git/med-team/quast/quast_libs/html_saver/html_saver.py", line 18, in <module> - from quast_libs.site_packages.jsontemplate import jsontemplate - File "/home/moeller/git/med-team/quast/quast_libs/site_packages/jsontemplate/jsontemplate.py", line 583, in <module> - 'html': cgi.escape, -AttributeError: module 'cgi' has no attribute 'escape' -ERROR! exception caught! - -In case you have troubles running QUAST, you can write to [email protected] -or report an issue on our GitHub repository https://github.com/ablab/quast/issues -Please provide us with quast.log file from the output directory. - ===================================== debian/control ===================================== @@ -10,7 +10,7 @@ Build-Depends: debhelper-compat (= 13), python3-setuptools, python3-simplejson, busco, - minimap2, + minimap2 <!nocheck>, tigr-glimmer, python3-matplotlib <!nocheck>, python3-joblib <!nocheck> ===================================== debian/patches/noBwa.patch ===================================== @@ -1,9 +1,9 @@ -Author: Steffen Moeller -Last-Update: 2020-06-24 18:05:32 +0200 -Description: Use Debian packaged bwa +Author: Steffen Moeller, Andreas Tille +Last-Update: Fri, 26 Jun 2020 11:35:10 +0200 +Description: Use Debian packaged bwa, minimap2 and tigr-glimmer ---- quast.orig/setup.py -+++ quast/setup.py +--- a/setup.py ++++ b/setup.py @@ -34,11 +34,10 @@ except: 'You may also use old-style installation scripts: ./install.sh or ./install_full.sh', exit_with_code=1) @@ -98,3 +98,45 @@ Description: Use Debian packaged bwa (full_install_tools if install_full else []) }, include_package_data=True, +--- a/quast_libs/ca_utils/misc.py ++++ b/quast_libs/ca_utils/misc.py +@@ -24,7 +24,7 @@ except ImportError: + from quast_libs import qconfig + from quast_libs.qutils import compile_tool, val_to_str, get_path_to_program + +-contig_aligner_dirpath = join(qconfig.LIBS_LOCATION, 'minimap2') ++contig_aligner_dirpath = '/usr/bin' + ref_labels_by_chromosomes = OrderedDict() + intergenomic_misassemblies_by_asm = {} + contigs_aligned_lengths = {} +--- a/quast_libs/glimmer.py ++++ b/quast_libs/glimmer.py +@@ -131,19 +131,14 @@ def predict_genes(index, contigs_fpath, + + + def compile_glimmer(logger, only_clean=False): +- tool_dirpath = os.path.join(qconfig.LIBS_LOCATION, 'glimmer') +- tool_src_dirpath = os.path.join(tool_dirpath, 'src') +- +- if not get_path_to_program('glimmerhmm', tool_dirpath): +- compile_tool('GlimmerHMM', tool_src_dirpath, ['../glimmerhmm'], logger=logger, only_clean=only_clean) +- return get_path_to_program('glimmerhmm', tool_dirpath) ++ return get_path_to_program('tigr-glimmer', 'usr/bin') + + + def do(contigs_fpaths, gene_lengths, out_dirpath): + logger.print_timestamp() + logger.main_info('Running GlimmerHMM...') + +- tool_dirpath = os.path.join(qconfig.LIBS_LOCATION, 'glimmer') ++ tool_dirpath = '/usr/bin' + tmp_dirpath = os.path.join(out_dirpath, 'tmp') + tool_exec_fpath = compile_glimmer(logger) + if not tool_exec_fpath: +@@ -179,4 +174,4 @@ def do(contigs_fpaths, gene_lengths, out + shutil.rmtree(tmp_dirpath) + + logger.main_info('Done.') +- return genes_by_labels +\ No newline at end of file ++ return genes_by_labels View it on GitLab: https://salsa.debian.org/med-team/quast/-/commit/55e0dd6a025551b29fdca415d31c3474e19d78fc -- View it on GitLab: https://salsa.debian.org/med-team/quast/-/commit/55e0dd6a025551b29fdca415d31c3474e19d78fc You're receiving this email because of your account on salsa.debian.org.
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