[med-svn] [Git][med-team/trinityrnaseq][master] 2 commits: Default to Python 3, as needed.
Michael R. Crusoe
gitlab at salsa.debian.org
Wed Jan 2 08:50:32 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / trinityrnaseq
Commits:
19afd712 by Michael R. Crusoe at 2019-01-02T07:34:27Z
Default to Python 3, as needed.
- - - - -
4bc652fe by Michael R. Crusoe at 2019-01-02T08:49:03Z
Use better Java version check from upstream
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/better_java_version_check
- + debian/patches/python3
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+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 at 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
=====================================
@@ -0,0 +1,60 @@
+Author: Michael R. Crusoe <michael.crusoe at 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
=====================================
@@ -0,0 +1,178 @@
+Author: Michael R. Crusoe <michael.crusoe at 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
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/compare/9b4be3dade72675dc28a0a78b30e4e802faf313e...4bc652fefe72ceb19a88dc7e7f5a5f52e4eb7734
--
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/compare/9b4be3dade72675dc28a0a78b30e4e802faf313e...4bc652fefe72ceb19a88dc7e7f5a5f52e4eb7734
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/20190102/1f921d57/attachment-0001.html>
More information about the debian-med-commit
mailing list