[med-svn] [transdecoder] 02/02: new upstream release
Michael Crusoe
misterc-guest at moszumanska.debian.org
Wed May 18 09:29:37 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to tag debian/2.1.0+dfsg-1
in repository transdecoder.
commit 9f60ceb17b22a3232e1cddbdf90ec8dfa8b66db4
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Tue May 17 03:01:49 2016 -0700
new upstream release
---
debian/changelog | 7 ++++++
debian/patches/cd-hit-est-rename | 2 +-
debian/patches/fix-test | 14 ++++++++++++
debian/patches/reproducible-build | 33 ---------------------------
debian/patches/reproducible-sample_data.patch | 14 ++++++------
debian/patches/series | 2 +-
debian/rules | 2 +-
debian/transdecoder-doc.docs | 1 -
debian/transdecoder-doc.lintian-overrides | 25 ++++++++++++++++----
9 files changed, 51 insertions(+), 49 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 61f9a4a..168f57e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+transdecoder (2.1.0+dfsg-1) unstable; urgency=medium
+
+ * New upstream release
+ * Drop 'reproducible-build' patch, incorprorated upstream
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Wed, 18 May 2016 02:28:29 -0700
+
transdecoder (2.0.1+dfsg-3) unstable; urgency=medium
[ Eduard Sanou ]
diff --git a/debian/patches/cd-hit-est-rename b/debian/patches/cd-hit-est-rename
index e1a02e6..118ca55 100644
--- a/debian/patches/cd-hit-est-rename
+++ b/debian/patches/cd-hit-est-rename
@@ -4,7 +4,7 @@ Description: Fix path to Debian location of cd-hit-est
--- transdecoder.orig/TransDecoder.Predict
+++ transdecoder/TransDecoder.Predict
-@@ -56,7 +56,7 @@
+@@ -58,7 +58,7 @@
$ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
diff --git a/debian/patches/fix-test b/debian/patches/fix-test
new file mode 100644
index 0000000..e76572c
--- /dev/null
+++ b/debian/patches/fix-test
@@ -0,0 +1,14 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Description: Fix tests
+--- transdecoder.orig/Makefile
++++ transdecoder/Makefile
+@@ -8,6 +8,7 @@
+ cd ./sample_data && ./cleanme.pl
+
+ test:
+- cd ./sample_data/ && ./runMe.sh
+-
++ cd sample_data/cufflinks_example && ./runMe.sh
++ cd sample_data/pasa_example && ./runMe.sh
++ cd sample_data/simple_transcriptome_target && ./runMe.sh
+
diff --git a/debian/patches/reproducible-build b/debian/patches/reproducible-build
deleted file mode 100644
index f5af92c..0000000
--- a/debian/patches/reproducible-build
+++ /dev/null
@@ -1,33 +0,0 @@
-From b0525d572b8e8528ad19e919f6943d234d3281d1 Mon Sep 17 00:00:00 2001
-From: Charles Plessy <plessy at debian.org>
-Date: Mon, 28 Dec 2015 11:37:23 +0900
-Subject: [PATCH] Make output reproducible.
-
-Author: Chris Lamb <lamby at debian.org>
-Bug-Debian: #809187
-Forwarded: https://github.com/TransDecoder/TransDecoder/pull/10
----
- util/cufflinks_gtf_to_bed.pl | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/util/cufflinks_gtf_to_bed.pl b/util/cufflinks_gtf_to_bed.pl
-index 28547ba..8bbb4ed 100755
---- a/util/cufflinks_gtf_to_bed.pl
-+++ b/util/cufflinks_gtf_to_bed.pl
-@@ -68,11 +68,11 @@ main: {
-
- my $genes_href = $genome_trans_to_coords{$scaff};
-
-- foreach my $gene_id (keys %$genes_href) {
-+ foreach my $gene_id (sort keys %$genes_href) {
-
- my $trans_href = $genes_href->{$gene_id};
-
-- foreach my $trans_id (keys %$trans_href) {
-+ foreach my $trans_id (sort keys %$trans_href) {
-
- my $coords_href = $trans_href->{$trans_id};
-
---
-2.1.4
-
diff --git a/debian/patches/reproducible-sample_data.patch b/debian/patches/reproducible-sample_data.patch
index 773faec..4fc44ea 100644
--- a/debian/patches/reproducible-sample_data.patch
+++ b/debian/patches/reproducible-sample_data.patch
@@ -3,14 +3,14 @@ Description: Make the sample data reproducible
to get reproducible results
Author: Eduard Sanou <dhole at openmailbox.org>
Forwarded: https://github.com/TransDecoder/TransDecoder/pull/20
---- transdecoder-2.0.1+dfsg.orig/sample_data/runMe.sh
-+++ transdecoder-2.0.1+dfsg/sample_data/runMe.sh
-@@ -26,7 +26,7 @@ fi
- ../util/cufflinks_gtf_to_alignment_gff3.pl transcripts.gtf > transcripts.gff3
+--- transdecoder.orig/sample_data/cufflinks_example/runMe.sh
++++ transdecoder/sample_data/cufflinks_example/runMe.sh
+@@ -25,7 +25,7 @@
+ ../../util/cufflinks_gtf_to_alignment_gff3.pl transcripts.gtf > transcripts.gff3
## generate transcripts fasta file
--../util/cufflinks_gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta
-+PERL_HASH_SEED=0 ../util/cufflinks_gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta
+-../../util/cufflinks_gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta
++PERL_HASH_SEED=0 ../../util/cufflinks_gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta
## Extract the long ORFs
- ../TransDecoder.LongOrfs -t transcripts.fasta
+ ../../TransDecoder.LongOrfs -t transcripts.fasta
diff --git a/debian/patches/series b/debian/patches/series
index 8488ccc..1d2ac85 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,4 @@
+fix-test
cd-hit-est-rename
fix-whatis
-reproducible-build
reproducible-sample_data.patch
diff --git a/debian/rules b/debian/rules
index a00cfcb..e9af788 100755
--- a/debian/rules
+++ b/debian/rules
@@ -8,7 +8,7 @@ VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//'
dh $@ --parallel
override_dh_auto_clean:
- cd ./sample_data && ./cleanme.pl
+ cd ./sample_data && ./*/cleanme.pl
override_dh_auto_build:
diff --git a/debian/transdecoder-doc.docs b/debian/transdecoder-doc.docs
index 600b156..0fb2340 100644
--- a/debian/transdecoder-doc.docs
+++ b/debian/transdecoder-doc.docs
@@ -1,3 +1,2 @@
README
debian/tests/run-tests
-Release.Notes
diff --git a/debian/transdecoder-doc.lintian-overrides b/debian/transdecoder-doc.lintian-overrides
index c0d0003..1c50223 100644
--- a/debian/transdecoder-doc.lintian-overrides
+++ b/debian/transdecoder-doc.lintian-overrides
@@ -1,7 +1,22 @@
# Verbose copies from upstream tarball
-transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/blastp.results.outfmt6.gz
-transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/pfam.domtblout.gz
-transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/test.genome.fasta.gz
-transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/test.tophat.sam.gz
-transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/transcripts.gtf.gz
+transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/cufflinks_example/blastp.results.outfmt6.gz
+transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/cufflinks_example/pfam.domtblout.gz
+transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/cufflinks_example/blastp.results.outfmt6.gz
+transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/cufflinks_example/pfam.domtblout.gz
+transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/cufflinks_example/pfam.domtblout.gz
+transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/cufflinks_example/pfam.domtblout.gz
+transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/cufflinks_example/test.genome.fasta.gz
+transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/cufflinks_example/test.genome.fasta.gz
+transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/cufflinks_example/test.tophat.sam.gz
+transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/cufflinks_example/test.tophat.sam.gz
+transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/cufflinks_example/transcripts.gtf.gz
+transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/cufflinks_example/transcripts.gtf.gz
+transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/pasa_example/genome.fasta.gz
+transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/pasa_example/genome.fasta.gz
+transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/pasa_example/pasa_assemblies.fasta.gz
+transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/pasa_example/pasa_assemblies.fasta.gz
+transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/pasa_example/pasa_assemblies.gff3.gz
+transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/pasa_example/pasa_assemblies.gff3.gz
+transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.gz
+transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.gz
--
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