From 87c578c11c2bb8dd0fb8e18d7c48e3e179b144b8 Mon Sep 17 00:00:00 2001
From: Alexey Gurevich <alexeigurevich@gmail.com>
Date: Thu, 28 Dec 2017 17:48:32 +0300
Subject: [PATCH] Temp: disable gnuplot

---
 quast_libs/ca_utils/align_contigs.py | 5 +++--
 quast_libs/contigs_analyzer.py       | 4 ++--
 setup.py                             | 8 ++++----
 3 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/quast_libs/ca_utils/align_contigs.py b/quast_libs/ca_utils/align_contigs.py
index 05c484f..cc474c9 100644
--- a/quast_libs/ca_utils/align_contigs.py
+++ b/quast_libs/ca_utils/align_contigs.py
@@ -208,7 +208,8 @@ def align_contigs(nucmer_fpath, ref_fpath, contigs_fpath, old_contigs_fpath, ind
         shutil.move(filtered_delta_fpath, delta_fpath)
 
         if qconfig.draw_plots:
-            draw_mummer_plot(logger, nucmer_fpath, delta_fpath, index, log_out_f, log_err_f)
+        #    draw_mummer_plot(logger, nucmer_fpath, delta_fpath, index, log_out_f, log_err_f)
+            logger.warning("  " + qutils.index_to_str(index) + "Drawing MUMmer plots is disabled in QUAST's Bioconda package.")
 
         tmp_coords_fpath = coords_fpath + '_tmp'
 
@@ -262,4 +263,4 @@ def align_contigs(nucmer_fpath, ref_fpath, contigs_fpath, old_contigs_fpath, ind
                     return NucmerStatus.ERROR
 
         create_nucmer_successful_check(nucmer_successful_check_fpath, old_contigs_fpath, ref_fpath)
-    return NucmerStatus.OK
\ No newline at end of file
+    return NucmerStatus.OK
diff --git a/quast_libs/contigs_analyzer.py b/quast_libs/contigs_analyzer.py
index 5d1a789..e548ab8 100644
--- a/quast_libs/contigs_analyzer.py
+++ b/quast_libs/contigs_analyzer.py
@@ -257,8 +257,8 @@ def do(reference, contigs_fpaths, is_cyclic, output_dir, old_contigs_fpaths, bed
         logger.main_info('Failed aligning the contigs for all the assemblies. Only basic stats are going to be evaluated.')
         return dict(zip(contigs_fpaths, [NucmerStatus.FAILED] * len(contigs_fpaths))), None
 
-    if qconfig.draw_plots:
-        compile_gnuplot(logger, only_clean=False)
+    #if qconfig.draw_plots:
+    #    compile_gnuplot(logger, only_clean=False)
 
     num_nf_errors = logger._num_nf_errors
     create_nucmer_output_dir(output_dir)
diff --git a/setup.py b/setup.py
index 3c3949d..3b51479 100755
--- a/setup.py
+++ b/setup.py
@@ -63,7 +63,7 @@ if abspath(dirname(__file__)) != abspath(os.getcwd()):
 if cmd_in(['clean', 'sdist']):
     logger.info('Cleaning up binary files...')
     compile_aligner(logger, only_clean=True)
-    compile_gnuplot(logger, only_clean=True)
+    #compile_gnuplot(logger, only_clean=True)
     compile_glimmer(logger, only_clean=True)
     compile_gage(only_clean=True)
     compile_bwa(logger, only_clean=True)
@@ -160,9 +160,9 @@ if cmd_in(['install', 'develop', 'build', 'build_ext']):
     logger.info('* Compiling aligner *')
     if not compile_aligner(logger):
         modules_failed_to_install.append('Contigs aligners for reference-based evaluation (affects -R and many other options)')
-    logger.info('* Compiling gnuplot *')
-    if not compile_gnuplot(logger):
-        logger.warning('Cannot compile gnuplot. MUMmer plots will not be drawn')
+    #logger.info('* Compiling gnuplot *')
+    #if not compile_gnuplot(logger):
+    #    logger.warning('Cannot compile gnuplot. MUMmer plots will not be drawn')
     logger.info('* Compiling Glimmer *')
     if not compile_glimmer(logger):
         modules_failed_to_install.append('Glimmer gene-finding tool (affects --glimmer option)')
-- 
2.7.2

