Update to version 1.15.0.

3 files changed, 34 insertions, 16 deletions

diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile
index 10366124cbc3..cf5b58784fec 100644
--- a/biology/ugene/Makefile
+++ b/biology/ugene/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	ugene
-DISTVERSION=	1.14.2
+DISTVERSION=	1.15.0
 CATEGORIES=	biology science
 MASTER_SITES=	http://ugene.unipro.ru/downloads/
 DISTFILES=	${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \
@@ -74,10 +74,8 @@ post-patch:
 .for x in ugenecl ugeneui plugins_checker
 	@${ECHO_CMD} 'LIBS += -lexecinfo' >> ${WRKSRC}/src/${x}/${x}.pro
 .endfor
-# missing linefeeds at EOF irk gcc4.2
-	@(cd ${WRKSRC}/src && ${FIND} -E . -type f -regex '.*\.(cpp|h)' | \
-	while read f; do if [ "`${TAIL} -c 1 "$$f"`" ]; then \
-		${ECHO_CMD} >&2 "$${f#./} lacks newline at EOF, fixing"; \
-		${ECHO_CMD} >> "$$f"; fi; done)
+# remove BOM that gcc4.2 trips upon
+	@env LANG=C ${REINPLACE_CMD} -e 's,^...,,' \
+		${WRKSRC}/src/include/U2Formats/MysqlUpgradeTask.h
 
 .include <bsd.port.post.mk>
diff --git a/biology/ugene/distinfo b/biology/ugene/distinfo
index 505e3811b67b..5825859b8ff3 100644
--- a/biology/ugene/distinfo
+++ b/biology/ugene/distinfo
@@ -1,5 +1,5 @@
-SHA256 (ugene/ugene-1.14.2.tar.gz) = deea01b9a5386094fa2d7e48db9d529afd9520ed0d6bc5bb2fb40493ae861a3a
-SIZE (ugene/ugene-1.14.2.tar.gz) = 19800763
+SHA256 (ugene/ugene-1.15.0.tar.gz) = 8ab1bd3009a568c2d2d8176bb4b038891b231fe930f31a9568852773f9c10b36
+SIZE (ugene/ugene-1.15.0.tar.gz) = 20197629
 SHA256 (ugene/QueryDesigner_UserManual.pdf) = 2add11809ecc3225abfef417ad8d5435fed76a662081f461abb36e3d4b31cfcd
 SIZE (ugene/QueryDesigner_UserManual.pdf) = 824781
 SHA256 (ugene/UniproUGENE_UserManual.pdf) = c4aa20246988978c6b40a06f7753f78d204ee3155cb8876a3d665b9ebf5641db
diff --git a/biology/ugene/pkg-plist b/biology/ugene/pkg-plist
index 8415e70398d6..b85e0220a2a4 100644
--- a/biology/ugene/pkg-plist
+++ b/biology/ugene/pkg-plist
@@ -201,6 +201,10 @@ lib/ugene/plugins/liborf_marker.so
 lib/ugene/plugins/liborf_marker.so.1
 lib/ugene/plugins/liborf_marker.so.1.0
 lib/ugene/plugins/liborf_marker.so.1.0.0
+lib/ugene/plugins/libpcr.so
+lib/ugene/plugins/libpcr.so.1
+lib/ugene/plugins/libpcr.so.1.0
+lib/ugene/plugins/libpcr.so.1.0.0
 lib/ugene/plugins/libperf_monitor.so
 lib/ugene/plugins/libperf_monitor.so.1
 lib/ugene/plugins/libperf_monitor.so.1.0
@@ -245,10 +249,6 @@ lib/ugene/plugins/libsmith_waterman.so
 lib/ugene/plugins/libsmith_waterman.so.1
 lib/ugene/plugins/libsmith_waterman.so.1.0
 lib/ugene/plugins/libsmith_waterman.so.1.0.0
-lib/ugene/plugins/libsnp_effect.so
-lib/ugene/plugins/libsnp_effect.so.1
-lib/ugene/plugins/libsnp_effect.so.1.0
-lib/ugene/plugins/libsnp_effect.so.1.0.0
 lib/ugene/plugins/libtest_runner.so
 lib/ugene/plugins/libtest_runner.so.1
 lib/ugene/plugins/libtest_runner.so.1.0
@@ -275,6 +275,8 @@ lib/ugene/plugins/opencl_support.license
 lib/ugene/plugins/opencl_support.plugin
 lib/ugene/plugins/orf_marker.license
 lib/ugene/plugins/orf_marker.plugin
+lib/ugene/plugins/pcr.license
+lib/ugene/plugins/pcr.plugin
 lib/ugene/plugins/perf_monitor.license
 lib/ugene/plugins/perf_monitor.plugin
 lib/ugene/plugins/phylip.license
@@ -297,8 +299,6 @@ lib/ugene/plugins/sitecon.license
 lib/ugene/plugins/sitecon.plugin
 lib/ugene/plugins/smith_waterman.license
 lib/ugene/plugins/smith_waterman.plugin
-lib/ugene/plugins/snp_effect.license
-lib/ugene/plugins/snp_effect.plugin
 lib/ugene/plugins/test_runner.license
 lib/ugene/plugins/test_runner.plugin
 %%NOX64%%lib/ugene/plugins/umuscle.license
@@ -373,7 +373,9 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/cmdline/convert-seq.uwl
 %%DATADIR%%/cmdline/das_annotation.uwl
 %%DATADIR%%/cmdline/extract-sequence.uwl
-%%DATADIR%%/cmdline/extract_consensus.uwl
+%%DATADIR%%/cmdline/extract_consensus_sequence.uwl
+%%DATADIR%%/cmdline/extract_consensus_string.uwl
+%%DATADIR%%/cmdline/extract_coverage.uwl
 %%DATADIR%%/cmdline/fetch-sequence.uwl
 %%DATADIR%%/cmdline/find-orfs.uwl
 %%DATADIR%%/cmdline/find-repeats.uwl
@@ -1385,6 +1387,8 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/weight_matrix/vtml160.txt
 %%DATADIR%%/weight_matrix/vtml200.txt
 %%DATADIR%%/workflow_samples/Alignment/basic_align.uwl
+%%DATADIR%%/workflow_samples/Alignment/extract_msa_consensus_as_seq.uwl
+%%DATADIR%%/workflow_samples/Alignment/extract_msa_consensus_as_text.uwl
 %%DATADIR%%/workflow_samples/Conversions/faqual2fastq.uwl
 %%DATADIR%%/workflow_samples/Conversions/msa2clustal.uwl
 %%DATADIR%%/workflow_samples/Conversions/query2alignment.uwl
@@ -1401,12 +1405,28 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/workflow_samples/Data merging/tfbs.uwl
 %%DATADIR%%/workflow_samples/HMMER/build-test-HMM.uwl
 %%DATADIR%%/workflow_samples/HMMER/searchHMM.uwl
+%%DATADIR%%/workflow_samples/NGS/assembly/spades_paired.uwl
+%%DATADIR%%/workflow_samples/NGS/assembly/spades_single.uwl
+%%DATADIR%%/workflow_samples/NGS/assembly.uwl
 %%DATADIR%%/workflow_samples/NGS/call_variants.uwl
 %%DATADIR%%/workflow_samples/NGS/cistrome/chip_seq.uwl
 %%DATADIR%%/workflow_samples/NGS/cistrome/chip_seq_with_control.uwl
 %%DATADIR%%/workflow_samples/NGS/cistrome.uwl
 %%DATADIR%%/workflow_samples/NGS/consensus.uwl
+%%DATADIR%%/workflow_samples/NGS/chipseq_coverage.uwl
+%%DATADIR%%/workflow_samples/NGS/extract_coverage.uwl
 %%DATADIR%%/workflow_samples/NGS/extract_transcript_seq.uwl
+%%DATADIR%%/workflow_samples/NGS/raw_chip.uwl
+%%DATADIR%%/workflow_samples/NGS/raw_dna.uwl
+%%DATADIR%%/workflow_samples/NGS/raw_ngs/chipseq/chipseq_paired.uwl
+%%DATADIR%%/workflow_samples/NGS/raw_ngs/chipseq/chipseq_single.uwl
+%%DATADIR%%/workflow_samples/NGS/raw_ngs/dnaseq/dna_paired.uwl
+%%DATADIR%%/workflow_samples/NGS/raw_ngs/dnaseq/dna_single.uwl
+%%DATADIR%%/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_filtration_paired.uwl
+%%DATADIR%%/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_filtration_single.uwl
+%%DATADIR%%/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_paired.uwl
+%%DATADIR%%/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_single.uwl
+%%DATADIR%%/workflow_samples/NGS/raw_rna.uwl
 %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_main.uwl
 %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_main_paired.uwl
 %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr.uwl
@@ -1414,11 +1434,11 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset.uwl
 %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset_paired.uwl
 %%DATADIR%%/workflow_samples/NGS/tuxedo.uwl
-%%DATADIR%%/workflow_samples/Scenarios/extract_consensus.uwl
 %%DATADIR%%/workflow_samples/Scenarios/filter_matched.uwl
 %%DATADIR%%/workflow_samples/Scenarios/find_inverted_repeats.uwl
 %%DATADIR%%/workflow_samples/Scenarios/find_sequences.uwl
 %%DATADIR%%/workflow_samples/Scenarios/gene_by_gene_report.uwl
+%%DATADIR%%/workflow_samples/Scenarios/group_primers_pairs.uwl
 %%DATADIR%%/workflow_samples/Scenarios/merge_sequence_annotation.uwl
 %%DATADIR%%/workflow_samples/Scenarios/remote_blasting.uwl
 %%DATADIR%%/workflow_samples/Scenarios/translate_seq_and_compl.uwl