debian/changelog

+trinityrnaseq (2.6.6+dfsg-4) unstable; urgency=medium
+
+  * Default to Python 3, as needed.
+  * Use better Java version check from upstream
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 02 Jan 2019 00:48:52 -0800
+
 trinityrnaseq (2.6.6+dfsg-3) unstable; urgency=medium
 
   * debian/control: add numpy dependency, required for

debian/control

@@ -30,7 +30,6 @@ Depends: ${shlibs:Depends},
          ${java:Depends},
          bowtie,
          bowtie2,
-         python,
          libwww-perl,
          default-jre-headless,
          samtools,
@@ -45,7 +44,7 @@ Depends: ${shlibs:Depends},
          parafly,
          curl,
          salmon,
-	 python3-numpy | python-numpy
+	 python3-numpy
 Recommends: ${java:Recommends},
             trinityrnaseq-examples
 Suggests: collectl

debian/patches/better_java_version_check

+Author: Michael R. Crusoe <michael.crusoe@gmail.com>
+Description: Use updated Java version check from upstream
+--- trinityrnaseq.orig/Trinity
++++ trinityrnaseq/Trinity
+@@ -561,7 +561,7 @@
+ my $CHRYSALIS_DEBUG_WELD_ALL = 0;
+ my $iworm_opts = "";
+ 
+-my $bypass_java_version_check = 0;
++my $bypass_java_version_check = 1;
+ 
+ my $VERBOSE = 0;
+ 
+@@ -1028,24 +1028,33 @@
+     die "Error, must specify max memory for jellyfish to use, eg.  --max_memory 10G \n";
+ }
+ 
+-
+ ## Check Java version:
+ unless ($NO_RUN_INCHWORM_FLAG || $NO_RUN_CHRYSALIS_FLAG || $bypass_java_version_check || $TRINITY_COMPLETE_FLAG) {
+     my $java_version = `java -Xmx64m -version 2>&1 `;
++
++    unless ($java_version) {
++        die "Error, cannot detect java via. 'java -Xmx64m -version'";
++    }
++    
++    my $version_id;
+     if ($java_version =~ /(java|openjdk) version \"1\.(\d)\./) {
+-      my $version_id = $2;
+-      if ($version_id < $JAVA_VERSION_REQUIRED) {
+-          die "Error, Trinity requires access to Java version 1.$JAVA_VERSION_REQUIRED or higher.  Currently installed version is: $java_version";
+-      }
+-  }
+-  else {
+-      print STDERR "\n\n\n********************************************************************\n"
+-                       . "** Warning, Trinity cannot determine which version of Java is being used.  Version 1.$JAVA_VERSION_REQUIRED is required. \n\nAttempting to continue in 30 seconds\n"
+-                       . "********************************************************************\n\n\n";
+-      sleep(30);
+-  }
+-}
++        $version_id = $2;
++    }
++    elsif ($java_version =~ /java version \"(\d+)(\.)?([._\d])+?\" ?/) {
++        $version_id = $1;
++    }
++    elsif ($java_version =~ /java (\d+) /) {
++        $version_id = $1;
++    }
++    else {
++        die "Error, cannot extract java version info from: ($java_version) ...  run with --bypass_java_version_check if you're sure that you have at least java version: $JAVA_VERSION_REQUIRED installed ";
++    }
++    
++    if ($version_id < $JAVA_VERSION_REQUIRED) {
++        die "Error, Trinity requires access to Java version 1.$JAVA_VERSION_REQUIRED or higher.  Currently installed version is: $java_version";
++    }
+ 
++}
+ 
+ unless ($NO_VERSION_CHECK || $TRINITY_COMPLETE_FLAG) {
+     &version_check();

debian/patches/python3

+Author: Michael R. Crusoe <michael.crusoe@gmail.com>
+Description: Default to running Python 3
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py
++++ trinityrnaseq/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # encoding: utf-8
+ 
+ from __future__ import (absolute_import, division,
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py
++++ trinityrnaseq/Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # encoding: utf-8
+ 
+ from __future__ import (absolute_import, division,
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/extract_supertranscript_from_reference.py
++++ trinityrnaseq/Analysis/SuperTranscripts/extract_supertranscript_from_reference.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # encoding: utf-8
+ 
+ from __future__ import (absolute_import, division, print_function, unicode_literals)
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Compact_graph_partial.py
++++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Compact_graph_partial.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # encoding: utf-8
+ 
+ from __future__ import (absolute_import, division,
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Compact_graph_whole.py
++++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Compact_graph_whole.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # encoding: utf-8
+ 
+ from __future__ import (absolute_import, division,
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/DP_matrix.py
++++ trinityrnaseq/Analysis/SuperTranscripts/pylib/DP_matrix.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # encoding: utf-8
+ 
+ from __future__ import (absolute_import, division,
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Gene_splice_modeler.py
++++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Gene_splice_modeler.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # encoding: utf-8
+ 
+ from __future__ import (absolute_import, division,
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/GraphCycleException.py
++++ trinityrnaseq/Analysis/SuperTranscripts/pylib/GraphCycleException.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # encoding: utf-8
+ 
+ from __future__ import (absolute_import, division,
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Node_alignment.py
++++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Node_alignment.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # encoding: utf-8
+ 
+ from __future__ import (absolute_import, division,
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Node_path.py
++++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Node_path.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # encoding: utf-8
+ 
+ from __future__ import (absolute_import, division,
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Splice_model_refiner.py
++++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Splice_model_refiner.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # encoding: utf-8
+ 
+ from __future__ import (absolute_import, division,
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/TGLOBALS.py
++++ trinityrnaseq/Analysis/SuperTranscripts/pylib/TGLOBALS.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ DEBUG = False
+ 
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/TGraph.py
++++ trinityrnaseq/Analysis/SuperTranscripts/pylib/TGraph.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # encoding: utf-8
+ 
+ from __future__ import (absolute_import, division,
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/TNode.py
++++ trinityrnaseq/Analysis/SuperTranscripts/pylib/TNode.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # encoding: utf-8
+ 
+ from __future__ import (absolute_import, division,
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Topological_sort.py
++++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Topological_sort.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # encoding: utf-8
+ 
+ from __future__ import (absolute_import, division,
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.py
++++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # encoding: utf-8
+ 
+ from __future__ import (absolute_import, division,
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Trinity_util.py
++++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Trinity_util.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # encoding: utf-8
+ 
+ from __future__ import (absolute_import, division,
+--- trinityrnaseq.orig/PyLib/Pipeliner.py
++++ trinityrnaseq/PyLib/Pipeliner.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # encoding: utf-8
+ 
+ from __future__ import (absolute_import, division,
+--- trinityrnaseq.orig/trinity-plugins/COLLECTL/util/collectl_dat_to_time_matrix.py
++++ trinityrnaseq/trinity-plugins/COLLECTL/util/collectl_dat_to_time_matrix.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # encoding: utf-8
+ 
+ from __future__ import (absolute_import, division,
+--- trinityrnaseq.orig/trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py
++++ trinityrnaseq/trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ import sys, collections, itertools, os.path, optparse
+ 
+--- trinityrnaseq.orig/util/misc/TPM_weighted_gene_length.py
++++ trinityrnaseq/util/misc/TPM_weighted_gene_length.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # encoding: utf-8
+ 
+ from __future__ import (absolute_import, division,
+--- trinityrnaseq.orig/util/support_scripts/trinity_installer.py
++++ trinityrnaseq/util/support_scripts/trinity_installer.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ import os, re, sys, subprocess
+ 

debian/patches/series

@@ -11,3 +11,5 @@ build_with_gcc6.patch
 NeedlemanWunschGotohBanded.patch
 disable-libieee
 # assume_modern_g++.patch
+python3
+better_java_version_check