Merge branch 'release-1.27' into release

.gitignore

@@ -35,10 +35,12 @@ Makefile.Debug
 # Jetbrains tools (CLion, etc..)
 .idea
 
-# Directories with tests and QSpec
+# Directories with tests
 /test
-/src/libs_3rdparty/QSpec/
 
 
 # QtCreator files
 ugene.pro.user
+
+# CLion build dir
+cmake-build-*

.gitmodules

@@ -0,0 +1,4 @@
+[submodule "QSpec"]
+	path = src/libs_3rdparty/QSpec
+	url = https://github.com/ugeneunipro/QSpec.git
+	branch = ugene

README.md

@@ -23,13 +23,17 @@ Make sure the Qt (>= 5.2.1 and < 5.6) development libraries are installed:
 To build with devenv (Visual Studio)
 
 1. `qmake -r -tp vc ugene.pro`
+   1.1. add "CONFIG+=x64" to qmake command for 64-bit build
 2. open ugene.sln from Visual Studio or run `devenv.exe ugene.sln /Build` from MSVC command line
 
 To build with nmake.exe:
 
 1. `qmake -r ugene.pro`
+   1.1. add "CONFIG+=x64" to qmake command for 64-bit build
 2. run `nmake`, `nmake debug` or `nmake release` to build UGENE
 
+Also you need to add "libeay.dll" and "ssleay.dll" from OpenSSL ToolKit to "../ugene/src/_debug" folder
+
 ### For *nix users:
 
 0. installation paths may be set up in ugene_globals.pri

data/cmdline/align-to-reference.uwl

@@ -0,0 +1,99 @@
+#@UGENE_WORKFLOW
+#The workflow does the following things:
+#1) Reads a set of Sanger sequencing reads from ABI files.
+#2) Trims ends of the reads by the quality value.
+#3) Filter the short trimmed reads.
+#4) Aligns the filtered trimmed reads to a reference sequence.
+#
+#You can change the workflow parameters:
+#1) Quality threshold for the trimming.
+#2) Minimum read length. If length of a trimmed read is less than the minimum value than the read is filtered.
+#
+#The output data are:
+#1) Multiple sequence alignment file. The first sequence of the alignment is the reference and other ones are the reads.
+#2) Annotated reference sequence file. The annotations are the aligned reads.
+
+
+
+workflow "Trim and map Sanger reads"{
+
+    SequenceQualityTrim {
+        type:SequenceQualityTrim;
+        name:"Sequence Quality Trimmer";
+    }
+    read-sequence {
+        type:read-sequence;
+        name:"Read Sequence";
+        url-in {
+            dataset:"Dataset 1";
+        }
+    }
+    align-to-reference {
+        type:align-to-reference;
+        name:"Map to Reference";
+        result-url:alignment.ugenedb;
+    }
+
+    .actor-bindings {
+        read-sequence.out-sequence->SequenceQualityTrim.in-sequence
+        SequenceQualityTrim.out-sequence->align-to-reference.in-sequence
+    }
+
+    read-sequence.sequence->SequenceQualityTrim.in-sequence.sequence
+    SequenceQualityTrim.sequence->align-to-reference.in-sequence.sequence
+
+    .meta {
+        parameter-aliases {
+            SequenceQualityTrim.both-ends {
+                alias:trim-both-ends;
+            }
+            SequenceQualityTrim.len-id {
+                alias:min-length;
+            }
+            SequenceQualityTrim.qual-id {
+                alias:threshold;
+            }
+            read-sequence.url-in {
+                alias:reads;
+            }
+            align-to-reference.identity {
+                alias:min-identity;
+            }
+            align-to-reference.reference {
+                alias:reference;
+            }
+            align-to-reference.result-url {
+                alias:result-url;
+            }
+        }
+        visual {
+            SequenceQualityTrim {
+                pos:"-705 -555";
+                style:ext;
+                bg-color-ext:"0 128 128 64";
+                in-sequence.angle:180;
+                out-sequence.angle:360;
+            }
+            align-to-reference {
+                pos:"-405 -540";
+                style:ext;
+                bg-color-ext:"0 128 128 64";
+                in-sequence.angle:180;
+                out.angle:360;
+            }
+            read-sequence {
+                pos:"-960 -540";
+                style:ext;
+                bg-color-ext:"0 128 128 64";
+                out-sequence.angle:360;
+            }
+            SequenceQualityTrim.out-sequence->align-to-reference.in-sequence {
+                text-pos:"-45 -43";
+            }
+            read-sequence.out-sequence->SequenceQualityTrim.in-sequence {
+                text-pos:"-33.8281 -27";
+            }
+        }
+    }
+}
+

data/cmdline/extract_consensus_sequence.uwl

@@ -57,7 +57,7 @@ workflow "New workflow"{
                 alias:keep_gaps;
             }
             extract-msa-consensus-sequence.threshold {
-                alias:threshhold;
+                alias:threshold;
             }
         }
         visual {

data/workflow_samples/Sanger sequencing/trim-and-align.uwl

@@ -15,173 +15,85 @@
 
 include "Read one sequence.usa" as "Script-Read one sequence"
 
-workflow "Trim and align Sanger reads"{
+workflow "Trim and map Sanger reads"{
 
-    QualityTrim {
-        type:QualityTrim;
-        name:"FASTQ Quality Trimmer";
+    SequenceQualityTrim {
+        type:SequenceQualityTrim;
+        name:"Sequence Quality Trimmer";
         both-ends:true;
         out-mode:1;
     }
-    get-file-list {
-        type:get-file-list;
-        name:"File List";
+    read-sequence {
+        type:read-sequence;
+        name:"Read Sequence";
         url-in {
             dataset:"Dataset 1";
         }
     }
-    files-conversion {
-        type:files-conversion;
-        name:"To FASTQ";
-        document-format:fastq;
-        out-mode:1;
-    }
-    Script-Read-sequence {
-        type:"Script-Read one sequence";
-        name:"Read sequence";
-        script {
-out_sequence = null;
-try {
-    var sequences = readSequences(in_text);
-    if (1 == sequences.length) {
-        out_sequence = sequences[0];
-    }
-} catch (e) {
-    print(e.toString());
-}
-        };
-    }
     align-to-reference {
         type:align-to-reference;
-        name:"Align to Reference";
-    }
-    write-msa {
-        type:write-msa;
-        name:"Write Alignment";
-        url-out:"alignment.aln";
-    }
-    write-sequence {
-        type:write-sequence;
-        name:"Write Sequence";
-        accumulate:false;
-        document-format:genbank;
-        url-out:"sequence.gb";
+        name:"Map to Reference";
+        result-url:alignment.ugenedb;
     }
 
     .actor-bindings {
-        get-file-list.out-url->files-conversion.in-file
-        QualityTrim.out-file->Script-Read-sequence.in
-        files-conversion.out-file->QualityTrim.in-file
-        Script-Read-sequence.out->align-to-reference.in-sequence
-        align-to-reference.out->write-msa.in-msa
-        align-to-reference.out->write-sequence.in-sequence
+        SequenceQualityTrim.out-sequence->align-to-reference.in-sequence
+        read-sequence.out-sequence->SequenceQualityTrim.in-sequence
     }
 
-    files-conversion.url->QualityTrim.in-file.url
-    get-file-list.url->files-conversion.in-file.url
-    QualityTrim.url->Script-Read-sequence.in.text
-    Script-Read-sequence.sequence->align-to-reference.in-sequence.sequence
-    align-to-reference.msa->write-msa.in-msa.msa
-    align-to-reference.annotations->write-sequence.in-sequence.annotations
-    align-to-reference.sequence->write-sequence.in-sequence.sequence
+    read-sequence.sequence->SequenceQualityTrim.in-sequence.sequence
+    SequenceQualityTrim.sequence->align-to-reference.in-sequence.sequence
 
     .meta {
         parameter-aliases {
-            QualityTrim.len-id {
+            SequenceQualityTrim.len-id {
                 alias:min-length;
             }
-            QualityTrim.qual-id {
+            SequenceQualityTrim.qual-id {
                 alias:threshold;
             }
-            get-file-list.url-in {
+            read-sequence.url-in {
                 alias:reads;
             }
             align-to-reference.reference {
                 alias:reference;
             }
-            write-msa.url-out {
-                alias:out-alignemnt;
-            }
-            write-msa.url-suffix {
-                alias:alignment-suffix;
-            }
-            write-sequence.url-out {
-                alias:out-seq;
-            }
-            write-sequence.url-suffix {
-                alias:seq-suffix;
+            align-to-reference.result-url {
+                alias:result-url;
             }
         }
         visual {
-            QualityTrim {
-                pos:"-585 -510";
+            SequenceQualityTrim {
+                pos:"-720 -570";
                 style:ext;
-                bg-color-ext:"208 69 0 64";
-                in-file.angle:180;
-                out-file.angle:296.206;
-            }
-            Script-Read-sequence {
-                pos:"-540 -300";
-                style:simple;
-                bg-color-simple:"84 84 84 255";
-                in.angle:93.6914;
-                out.angle:360;
+                bg-color-ext:"0 128 128 64";
+                in-sequence.angle:180;
+                out-sequence.angle:360;
             }
             align-to-reference {
-                pos:"-390 -300";
+                pos:"-420 -555";
                 style:ext;
-                bg-color-ext:"0 128 0 64";
+                bg-color-ext:"0 128 128 64";
                 in-sequence.angle:180;
                 out.angle:360;
             }
-            files-conversion {
-                pos:"-750 -510";
-                style:simple;
-                bg-color-simple:"84 84 84 255";
-                in-file.angle:177.917;
-                out-file.angle:360;
-            }
-            get-file-list {
-                pos:"-930 -510";
-                style:ext;
-                bg-color-ext:"24 102 175 64";
-                out-url.angle:353.118;
-            }
-            write-msa {
-                pos:"-120 -300";
-                style:ext;
-                bg-color-ext:"64 26 96 64";
-                in-msa.angle:180;
-            }
-            write-sequence {
-                pos:"-120 -510";
+            read-sequence {
+                pos:"-975 -555";
                 style:ext;
-                bg-color-ext:"64 26 96 64";
-                in-sequence.angle:180;
-            }
-            QualityTrim.out-file->Script-Read-sequence.in {
-                text-pos:"-31.5 -15";
-            }
-            Script-Read-sequence.out->align-to-reference.in-sequence {
-                text-pos:"-30.5 -28";
+                bg-color-ext:"0 128 128 64";
+                out-sequence.angle:360;
             }
-            align-to-reference.out->write-msa.in-msa {
-                text-pos:"-34 -24";
+            SequenceQualityTrim.out-sequence->align-to-reference.in-sequence {
+                text-pos:"-45 -43";
             }
-            align-to-reference.out->write-sequence.in-sequence {
-                text-pos:"-31 -11";
-            }
-            files-conversion.out-file->QualityTrim.in-file {
-                text-pos:"-12 -24";
-            }
-            get-file-list.out-url->files-conversion.in-file {
-                text-pos:"-31 -24";
+            read-sequence.out-sequence->SequenceQualityTrim.in-sequence {
+                text-pos:"-33.8281 -27";
             }
         }
         wizard {
-            help-page-id:16122701;    
+            help-page-id:16122701;
 	    auto-run: true;
-            name:"Trim and Align Sanger Reads";
+            name:"Trim and Map Sanger Reads";
             page {
                 id:1;
                 next:2;
@@ -201,7 +113,7 @@ try {
                 next:3;
                 title:"Input Sanger Reads (ABI Files)";
                 parameters-area {
-                    get-file-list.url-in {
+                    read-sequence.url-in {
                         type:datasets;
                     }
                 }
@@ -214,9 +126,9 @@ try {
                     group {
                         title:"Settings";
                         label-size:120;
-                        QualityTrim.qual-id {
+                        SequenceQualityTrim.qual-id {
                         }
-                        QualityTrim.len-id {
+                        SequenceQualityTrim.len-id {
                         }
                     }
                 }
@@ -228,11 +140,8 @@ try {
                     group {
                         title:"Output files";
                         label-size:120;
-                        write-msa.url-out {
-                            label:"Aligned reads file";
-                        }
-                        write-sequence.url-out {
-                            label:"Annotated sequence file";
+                        align-to-reference.result-url {
+                            label:"Mapped reads file";
                         }
                     }
                 }

installer/source/COPYRIGHT

@@ -1,5 +1,5 @@
 Unipro UGENE - Integrated Bioinformatics Suite
-Copyright (C) 2008-2016 Unipro, Novosibirsk, Russia
+Copyright (C) 2008-2017 Unipro, Novosibirsk, Russia
 
 This suite of programs is free software. You can redistribute it
 and/or modify it under the terms of the GNU General Public License as