[med-svn] [metabit] 02/06: New upstream version 0.0+20170220

[Andreas Tille]

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tille pushed a commit to branch master
in repository metabit.

commit b29df5feee89a1e92df695e6b738a182655bc29a
Author: Andreas Tille <tille at debian.org>
Date:   Wed May 10 15:08:01 2017 +0200

    New upstream version 0.0+20170220
---
 makefile.py                            |  8 +++++++-
 nodes/picard_simple.py                 |  4 ++++
 nodes/tools/statax_Rmodule/doBarplot.R | 13 +++++++------
 parts.py                               |  4 +++-
 4 files changed, 21 insertions(+), 8 deletions(-)

diff --git a/makefile.py b/makefile.py
index e44ad7b..64258c5 100644
--- a/makefile.py
+++ b/makefile.py
@@ -389,9 +389,15 @@ def _update_statax(makefile):
 
 def _update_metaphlan_options(makefile, config):
     """Applies metaphlan2 options if required"""
+
+    _, check_java=subprocess.Popen(["java", "-version"], stderr=subprocess.PIPE).communicate()
+    regexp = 'version "(\\d+).(\\d+)'
+    ## temp hack to avoid memory error for java 1.6 users.
+    if re.search(regexp, check_java).groups() == ('1','6'):
+        config.jre_options.append('-XX:MaxPermSize=1g')
+
     metaphlan_script = glob.glob(os.path.join(config.metaphlan_path,"metaphlan*.py"))[0]
     if metaphlan_script.endswith("metaphlan2.py"):
-        config.jre_options.append('-XX:MaxPermSize=1g')
         
         makefile['Metaphlan']['--mpa_pkl'] = os.path.join(config.metaphlan_path,
                                                           "db_v20/mpa_v20_m200.pkl")
diff --git a/nodes/picard_simple.py b/nodes/picard_simple.py
index 8a6d419..f55f64c 100644
--- a/nodes/picard_simple.py
+++ b/nodes/picard_simple.py
@@ -91,6 +91,10 @@ class MarkDuplicatesNode(PicardNode):
         params.set_option("METRICS_FILE", "%(OUT_METRICS)s", sep="=")
         #params.add_multiple_options("I", input_bams, sep="=")
         params.set_option("I", "%(IN_BAM)s", sep="=")
+        ## testing
+        # params.set_option("MAX_FILE_HANDLES_FOR_READ_ENDS_MAP", "16000", sep="=") 
+        # params.set_option("MAX_RECORDS_IN_RAM", "1000000", sep="=") 
+        # params.set_option("MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP", "100000", sep="=") 
 
         if not keep_dupes:
             # Remove duplicates from output by default to save disk-space
diff --git a/nodes/tools/statax_Rmodule/doBarplot.R b/nodes/tools/statax_Rmodule/doBarplot.R
index 32f5441..58b6411 100755
--- a/nodes/tools/statax_Rmodule/doBarplot.R
+++ b/nodes/tools/statax_Rmodule/doBarplot.R
@@ -55,11 +55,11 @@ doBarplot <- function(d, out.pdf=NULL,
   in.bp$labels <- gsub("\\s+", ".", in.bp$labels)
   in.bp$labels[in.bp$abundance < 4] <- ""
   in.bp[[legend.title]] <- factor(in.bp[[legend.title]],
-                                  levels=levels(in.bp[[legend.title]])[legend.order])
+                                  levels=unique(levels(in.bp[[legend.title]])[legend.order]))
 
   legend_text <- rownames(d)
   legend_cols <- split(legend_text, ceiling(seq_along(legend_text)/21))
-  #plot the stacked bar plot
+  #plot the stacked bar plots
   out.barplot <- ggplot(in.bp, aes_string(x="sample", y="abundance",
                                           label=legend.title)) + 
                  geom_bar(aes_string(fill=legend.title), stat="identity",
@@ -72,10 +72,11 @@ doBarplot <- function(d, out.pdf=NULL,
                  ggtitle(graph.title)
   if (add_labels) {
     out.barplot <- out.barplot + 
-                   geom_text(aes(label=labels, ymax=abundance, size=4, vjust=1),
-                             position=position_stack(),
-                             colour='white', alpha=.5) +
-                   scale_size(guide="none")
+        # geom_text(aes(label=labels, ymax=abundance, size=4, vjust=1),
+        geom_text(aes(label=labels, size=4, vjust=1),                  
+                  position=position_stack(),
+                  colour='white', alpha=.5) +
+        scale_size(guide="none")
   }
 
   # .3 inches ~= strheight
diff --git a/parts.py b/parts.py
index 4efe567..1b51bc3 100644
--- a/parts.py
+++ b/parts.py
@@ -314,7 +314,9 @@ def analyzing(makefile, config, metaphlan_nodes=(), group='all'):
                                description="<krona: ktImportText -> %s>" % output_file,
                                dependencies = krona_dep,
                                builder_kwargs={"OUT_FILE": output_file})
-        krona_node.command.set_option("-a", True, fixed=False)
+        ## fix to make it work with krona 2.7
+        makefile['Krona'].pop('-a', None)
+        # krona_node.command.set_option("-a", True, fixed=False)
         apply_options(krona_node.command, makefile['Krona'])
         krona_node.command.add_multiple_values(krona_input_files)
         

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