[med-svn] [Git][med-team/quast][master] Test suite is now running

[Andreas Tille]

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 at 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 quast.support at cab.spbu.ru
-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.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200626/0d847664/attachment-0001.html>