Merge branch 'release-1.31.0' into release

ugeneunipro · Aug 17, 2018 · 49f9a6a · 49f9a6a
2 parents ec84c57 + fd0175d
commit 49f9a6a
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diff --git a/.gitignore b/.gitignore
@@ -29,6 +29,12 @@ Makefile.Debug
 .qmake.stash
 *.xcodeproj/
 
+# Windows generated files
+*.obj
+**/Win32/Debug/*
+ugene.VC.db
+ugene.VC.VC.opendb
+
 # Generated ugene shell launcher
 /ugene
 
@@ -44,3 +50,9 @@ ugene.pro.user
 
 # CLion build dir
 cmake-build-*
+
+# Qt generated
+**/GeneratedFiles/*
+
+# NGS taxonomy and databases
+data/ngs_classification
diff --git a/.gitmodules b/.gitmodules
@@ -2,3 +2,4 @@
 	path = src/libs_3rdparty/QSpec
 	url = https://github.com/ugeneunipro/QSpec.git
 	branch = ugene
+	ignore = dirty
diff --git a/.travis.yml b/.travis.yml
@@ -7,7 +7,7 @@ install:
   - sudo apt-get update -qq
   - sudo apt-get install qtbase5-dev qtdeclarative5-dev libqt5webkit5-dev libsqlite3-dev libqt5svg5-dev
   - sudo apt-get install qt5-default qttools5-dev-tools qtscript5-dev
-  - sudo apt-get install libxtst-dev libprocps3-dev
+  - sudo apt-get install libxtst-dev
 
 script:
   - qmake ugene.pro CONFIG+=x64 UGENE_EXCLUDE_LIST_ENABLED=1 UGENE_USE_BUNDLED_ZLIB=0

diff --git a/README.md b/README.md
@@ -6,14 +6,12 @@
 
 Make sure the Qt (>= 5.2.1 and < 5.6) development libraries are installed:
 
-* Ubuntu 16.04: `sudo apt-get install qt5-default qttools5-dev-tools qtscript5-dev libqt5svg5-dev libqt5webkit5-dev libprocps4-dev`
-* Ubuntu 14.04: `sudo apt-get install qt5-default qttools5-dev-tools qtscript5-dev libqt5svg5-dev libqt5webkit5-dev libprocps3-dev`
+* Ubuntu >=14.04: `sudo apt-get install qt5-default qttools5-dev-tools qtscript5-dev libqt5svg5-dev libqt5webkit5-dev`
 * Ubuntu 12.04:
     * Download and install Qt 5.5.1: www.qt.io/download-open-source/
     * Set the system variable: export PATH=$PATH:~/Qt5.5.1/5.5/gcc_64/bin
-    * `sudo apt-get install g++ libgl1-mesa-dev libproc-dev libglu1-mesa-dev`
-    * `sudo ln -s /usr/lib/libproc.so /usr/lib/libprocps.so`
-* Fedora:       `sudo yum install qt5-qtscript-devel qt5-qtbase-devel qt5-qtsvg-devel qt5-linguist qt5-qtwebkit-devel gcc-c++ redhat-rpm-config procps-ng-devel mesa-libGLU-devel`
+    * `sudo apt-get install g++ libgl1-mesa-dev libglu1-mesa-dev`
+* Fedora:       `sudo yum install qt5-qtscript-devel qt5-qtbase-devel qt5-qtsvg-devel qt5-linguist qt5-qtwebkit-devel gcc-c++ redhat-rpm-config mesa-libGLU-devel`
 * Arch Linux:   `sudo pacman -S qt`
 * Mac OS X: download from Qt official site (http://www.qt.io/download/)
 * Windows: download from Qt official site (http://www.qt.io/download/)

diff --git a/build.txt b/build.txt
@@ -4,13 +4,11 @@ Prerequisites
 
 Make sure the Qt (>= 5.2.1 and < 5.6) development libraries are installed:
 
-* Ubuntu 16.04: `sudo apt-get install qt5-default qttools5-dev-tools qtscript5-dev libqt5svg5-dev libqt5webkit5-dev libprocps4-dev`
-* Ubuntu 14.04: `sudo apt-get install qt5-default qttools5-dev-tools qtscript5-dev libqt5svg5-dev libqt5webkit5-dev libprocps3-dev`
+* Ubuntu >=14.04: `sudo apt-get install qt5-default qttools5-dev-tools qtscript5-dev libqt5svg5-dev libqt5webkit5-dev`
 * Ubuntu 12.04: 1. Download and install Qt 5.5.1: www.qt.io/download-open-source/
                 2. Set the system variable: export PATH=$PATH:~/Qt5.5.1/5.5/gcc_64/bin
-                3. `sudo apt-get install g++ libgl1-mesa-dev libproc-dev libglu1-mesa-dev`
-                4. `sudo ln -s /usr/lib/libproc.so /usr/lib/libprocps.so`
-* Fedora:       `sudo yum install qt5-qtscript-devel qt5-qtbase-devel qt5-qtsvg-devel qt5-linguist qt5-qtwebkit-devel gcc-c++ redhat-rpm-config procps-ng-devel mesa-libGLU-devel`
+                3. `sudo apt-get install g++ libgl1-mesa-dev libglu1-mesa-dev`
+* Fedora:       `sudo yum install qt5-qtscript-devel qt5-qtbase-devel qt5-qtsvg-devel qt5-linguist qt5-qtwebkit-devel gcc-c++ redhat-rpm-config mesa-libGLU-devel`
 * Arch Linux:   `sudo pacman -S qt`
 * Mac OS X: download from Qt official site (http://www.qt.io/download/)
 * Windows: download from Qt official site (http://www.qt.io/download/)

diff --git a/data/DBXRefRegistry.txt b/data/DBXRefRegistry.txt
@@ -60,7 +60,7 @@ dictyBase|http://dictybase.org/db/cgi-bin/gene_page.pl?primary_id=%1||Dictyostel
 
 EcoGene|http://ecogene.org/geneInfo.php?eg_id=%1||Database of Escherichia coli Sequence and Function
 
-ENSEMBL|http://beta.rest.ensembl.org/sequence/id/%1?content-type=text/x-fasta|http://beta.rest.ensembl.org/sequence/id/%1?content-type=text/x-fasta|Database of automatically annotated genomic data
+ENSEMBL|https://rest.ensembl.org/sequence/id/%1?content-type=text/x-fasta|https://rest.ensembl.org/sequence/id/%1?content-type=text/x-fasta|Database of automatically annotated genomic data
 
 EnsemblGenomes|http://ensemblgenomes.org/search/eg/%1||Extending Ensembl across taxonomic space
 
@@ -208,7 +208,7 @@ SRPDB|||Signal Recognition Particle Database
 
 SubtiList|||Bacillus subtilis genome sequencing project
 
-SWISS-PROT|http://www.uniprot.org/uniprot/%1|http://www.uniprot.org/uniprot/%1.txt|The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data.
+SWISS-PROT|https://www.uniprot.org/uniprot/%1|https://www.uniprot.org/uniprot/%1.txt|The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data.
 
 TAIR|||Arabidopsis IR
 
@@ -220,9 +220,9 @@ TubercuList|http://tuberculist.epfl.ch/quicksearch.php?gene+name=%1||TubercuList
 
 UNILIB|||Unified Library Database, a library-level view of the EST and SAGE libraries present in dbEST, UniGene and SAGEmap
 
-UniProtKB/Swiss-Prot|http://www.uniprot.org/uniprot/%1|http://www.uniprot.org/uniprot/%1.txt|section of the UniProt Knowledgebase, containing annotated records
+UniProtKB/Swiss-Prot|https://www.uniprot.org/uniprot/%1|https://www.uniprot.org/uniprot/%1.txt|section of the UniProt Knowledgebase, containing annotated records
 
-UniProtKB/TrEMBL|http://www.uniprot.org/uniprot/%1|http://www.uniprot.org/uniprot/%1.txt|section of the UniProt Knowledgebase, containing computationally analysed records waiting for full manual annotation
+UniProtKB/TrEMBL|https://www.uniprot.org/uniprot/%1|https://www.uniprot.org/uniprot/%1.txt|section of the UniProt Knowledgebase, containing computationally analysed records waiting for full manual annotation
 
 UniSTS|https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=%1||NCBI UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments.
 

diff --git a/data/adapters/illumina/NexteraPE-PE.fa b/data/adapters/illumina/NexteraPE-PE.fa
@@ -0,0 +1,12 @@
+>PrefixNX/1
+AGATGTGTATAAGAGACAG
+>PrefixNX/2
+AGATGTGTATAAGAGACAG
+>Trans1
+TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
+>Trans1_rc
+CTGTCTCTTATACACATCTGACGCTGCCGACGA
+>Trans2
+GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
+>Trans2_rc
+CTGTCTCTTATACACATCTCCGAGCCCACGAGAC
diff --git a/data/adapters/illumina/TruSeq2-PE.fa b/data/adapters/illumina/TruSeq2-PE.fa
@@ -0,0 +1,16 @@
+>PrefixPE/1
+AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>PrefixPE/2
+CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+>PCR_Primer1
+AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>PCR_Primer1_rc
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
+>PCR_Primer2
+CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+>PCR_Primer2_rc
+AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG
+>FlowCell1
+TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC
+>FlowCell2
+TTTTTTTTTTCAAGCAGAAGACGGCATACGA
diff --git a/data/adapters/illumina/TruSeq2-SE.fa b/data/adapters/illumina/TruSeq2-SE.fa
@@ -0,0 +1,6 @@
+>TruSeq2_SE
+AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
+>TruSeq2_PE_f
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
+>TruSeq2_PE_r
+AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
diff --git a/data/adapters/illumina/TruSeq3-PE-2.fa b/data/adapters/illumina/TruSeq3-PE-2.fa
@@ -0,0 +1,12 @@
+>PrefixPE/1
+TACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>PrefixPE/2
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+>PE1
+TACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>PE1_rc
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
+>PE2
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+>PE2_rc
+AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
diff --git a/data/adapters/illumina/TruSeq3-PE.fa b/data/adapters/illumina/TruSeq3-PE.fa
@@ -0,0 +1,4 @@
+>PrefixPE/1
+TACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>PrefixPE/2
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
diff --git a/data/adapters/illumina/TruSeq3-SE.fa b/data/adapters/illumina/TruSeq3-SE.fa
@@ -0,0 +1,4 @@
+>TruSeq3_IndexedAdapter
+AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
+>TruSeq3_UniversalAdapter
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
diff --git a/data/workflow_samples/Alignment/basic_align.uwl b/data/workflow_samples/Alignment/basic_align.uwl
@@ -59,6 +59,7 @@ workflow "Align sequences with MUSCLE"{
         wizard {
             name:"Align Sequences with MUSCLE Wizard";
             help-page-id:16122700;
+            auto-run: true;
             page {
                 id:1;
                 next:2;

diff --git a/data/workflow_samples/Alignment/extract_msa_consensus_as_seq.uwl b/data/workflow_samples/Alignment/extract_msa_consensus_as_seq.uwl
@@ -93,6 +93,7 @@ url_out = dir + "_consensus.fa"
         wizard {
             name:"Extract Alignment Consensus as Sequence";
             help-page-id:16122701;
+            auto-run: true;
             page {
                 id:1;
                 next:2;

diff --git a/data/workflow_samples/Alignment/extract_msa_consensus_as_text.uwl b/data/workflow_samples/Alignment/extract_msa_consensus_as_text.uwl
@@ -91,6 +91,7 @@ url_out = dir + "_consensus.txt"
         wizard {
             name:"Extract Alignment Consensus as Text";
             help-page-id:16122702;
+            auto-run: true;
             page {
                 id:1;
                 next:2;

diff --git a/data/workflow_samples/Conversions/faqual2fastq.uwl b/data/workflow_samples/Conversions/faqual2fastq.uwl
@@ -68,6 +68,7 @@ workflow "Convert seq/qual pair to FASTQ"{
         wizard {
             name:"Convert seq/qual pair to FASTQ Wizard";
             help-page-id:16122704;
+            auto-run: true;
             page {
                 id:1;
                 next:2;

diff --git a/data/workflow_samples/Conversions/msa2clustal.uwl b/data/workflow_samples/Conversions/msa2clustal.uwl
@@ -42,6 +42,7 @@ workflow "Convert alignments to ClustalW"{
         wizard {
             name:"Convert alignments to ClustalW Wizard";
             help-page-id:16122705;
+            auto-run: true;
             page {
                 id:1;
                 next:2;

diff --git a/data/workflow_samples/Conversions/query2alignment.uwl b/data/workflow_samples/Conversions/query2alignment.uwl
@@ -116,6 +116,7 @@ workflow "Convert UQL schema results to alignment" {
         wizard {
             name:"Convert UQL schema results to alignment Wizard";
             help-page-id:16122706;
+            auto-run: true;
             page {
                 id:1;
                 next:2;

diff --git a/data/workflow_samples/Conversions/seq2gen.uwl b/data/workflow_samples/Conversions/seq2gen.uwl
@@ -45,6 +45,7 @@ workflow "Convert sequence to Genbank"{
         wizard {
             name:"Convert sequence to Genbank Wizard";
             help-page-id:16122707;
+            auto-run: true;
             page {
                 id:1;
                 next:2;

diff --git a/data/workflow_samples/Custom elements/script-dump-sequence-info.uwl b/data/workflow_samples/Custom elements/script-dump-sequence-info.uwl
@@ -57,6 +57,7 @@ out_text=getName(in_sequence) + ": " + size(in_sequence);
         wizard {
             name:"Dump sequence info Wizard";
             help-page-id:16122709;
+            auto-run: true;
             page {
                 id:1;
                 next:2;

diff --git a/data/workflow_samples/Custom elements/script-linkdata-fetch-seq.uwl b/data/workflow_samples/Custom elements/script-linkdata-fetch-seq.uwl
@@ -51,6 +51,7 @@ out_sequence = sequenceFromText(LinkData.getObjects(workId,filename,subject,prop
         wizard {
             name:"LinkData fetch Wizard";
             help-page-id:16122710;
+            auto-run: true;
             page {
                 id:1;
                 title:"LinkData Fetch";

diff --git a/data/workflow_samples/Custom elements/script-quality-filter.uwl b/data/workflow_samples/Custom elements/script-quality-filter.uwl
@@ -76,6 +76,7 @@ out_sequence = null;
         wizard {
             name:"Quality filter Wizard";
             help-page-id:16122711;
+            auto-run: true;
             page {
                 id:1;
                 next:2;

diff --git a/data/workflow_samples/Data merging/find-substrings.uwl b/data/workflow_samples/Data merging/find-substrings.uwl
@@ -137,6 +137,7 @@ workflow "Find substrings in sequences"{
         wizard {
             name:"Find substrings in sequences Wizard";
             help-page-id:16122696;
+            auto-run: true;
             page {
                 id:1;
                 next:2;

diff --git a/data/workflow_samples/Data merging/tfbs.uwl b/data/workflow_samples/Data merging/tfbs.uwl
@@ -65,17 +65,13 @@ workflow "Search for tfbs"{
     .meta {
         visual {
             read-sequence {
-                description:"<!DOCTYPE HTML PUBLIC '-//W3C//DTD HTML 4.0//EN' 'http://www.w3.org/TR/REC-html40/strict.dtd'> <html><head><meta name='qrichtext' content='1' /><style type='text/css'> p, li { white-space: pre-wrap; } </style></head><body style=' font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;'> <p align='center' style=' margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;'><span style=' font-weight:600;'>Read Sequence</span></p> <hr /> <p style=' margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;'>Reads sequence(s) from <a href='param:url-in'><span style=' text-decoration: underline; color:#ff0000;'>unset</span></a>.</p></body></html>";
-                tooltip:"Reads sequences and annotations if any from local or remote files.";
                 pos:"-892 -468";
                 style:ext;
                 bg-color-ext:"0 128 128 64";
                 bounds:"-30 -30 150.25 44";
                 out-sequence.angle:357.083;
             }
             write-sequence {
-                description:"<!DOCTYPE HTML PUBLIC '-//W3C//DTD HTML 4.0//EN' 'http://www.w3.org/TR/REC-html40/strict.dtd'> <html><head><meta name='qrichtext' content='1' /><style type='text/css'> p, li { white-space: pre-wrap; } </style></head><body style=' font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;'> <p align='center' style=' margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;'><span style=' font-weight:600;'>Write Sequence</span></p> <hr /> <p style=' margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;'>Save all sequences from <span style=' text-decoration: underline;'>Read Sequence</span> to <a href='param:url-out'><span style=' text-decoration: underline; color:#ff0000;'>unset</span></a>.</p></body></html>";
-                tooltip:"Writes all supplied sequences to file(s) in selected format.";
                 pos:"-159.25 -474";
                 style:ext;
                 bg-color-ext:"0 128 128 64";
@@ -148,6 +144,7 @@ workflow "Search for tfbs"{
         wizard {
             name:"Search for tfbs Wizard";
             help-page-id:16122698;
+            auto-run: true;
             page {
                 id:1;
                 next:2;

diff --git a/data/workflow_samples/HMMER/build-test-HMM.uwl b/data/workflow_samples/HMMER/build-test-HMM.uwl
@@ -115,6 +115,7 @@ workflow "Build HMM from alignment and test it"{
         wizard {
             name:"Build HMM from alignment and test it Wizard";
             help-page-id:16122715;
+            auto-run: true;
             page {
                 id:1;
                 next:2;

diff --git a/data/workflow_samples/HMMER/searchHMM.uwl b/data/workflow_samples/HMMER/searchHMM.uwl
@@ -76,6 +76,7 @@ workflow "Search sequences with profile HMM"{
         wizard {
             name:"Search sequences with profile HMM Wizard";
             help-page-id:16122716;
+            auto-run: true;
             page {
                 id:1;
                 next:2;