Commit c3b401d5 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 33.0+dfsg

parent e586841c

.gitignore

+5 −3
Original line number Diff line number Diff line
@@ -2,6 +2,8 @@ 
**/_tmp

src/_debug

src/_release

src/qmake_msvc_proj_x32.cmd

src/qmake_msvc_proj_x64.cmd



# Makefiles generated by qmake

Makefile
@@ -16,7 +18,8 @@ Makefile.Debug 
# Doxygen generated files

/html



# VS project files

# VS project files and directories

/.vs/

*.sdf

*.opensdf

*.suo
@@ -31,8 +34,7 @@ Makefile.Debug 


# Windows generated files

*.obj

**/Win32/Debug/*

ugene.VC.db

*moc_predefs.h*ugene.VC.db

ugene.VC.VC.opendb



# Generated ugene shell launcher

.gitmodules

deleted100644 → 0
+0 −5
Original line number Diff line number Diff line 
[submodule "QSpec"]

	path = src/libs_3rdparty/QSpec

	url = https://github.com/ugeneunipro/QSpec.git

	branch = ugene

	ignore = dirty
 
 No newline at end of file

README.md

+1 −1
Original line number Diff line number Diff line
@@ -4,7 +4,7 @@ 


### Prerequisites



Make sure the Qt (>= 5.2.1 and < 5.6) development libraries are installed:

Make sure the Qt (>= 5.3.2) development libraries are installed:



* Ubuntu >=14.04: `sudo apt-get install qt5-default qttools5-dev-tools qtscript5-dev libqt5svg5-dev libqt5webkit5-dev`

* Ubuntu 12.04:

data/workflow_samples/NGS/fastqc.uwl

+5 −7
Original line number Diff line number Diff line
@@ -8,7 +8,6 @@ workflow "Quality control by FastQC"{ 
    fastqc {

        type:fastqc;

        name:"FastQC Quality Control";

        out-mode:1;

    }

    get-file-list {

        type:get-file-list;
@@ -29,8 +28,8 @@ workflow "Quality control by FastQC"{ 
            fastqc.contaminants {

                alias:c;

            }

            fastqc.custom-dir {

                alias:out_dir;

            fastqc.out-file {

                alias:out_file;

            }

            fastqc.out-mode {

                alias:mode;
@@ -41,13 +40,13 @@ workflow "Quality control by FastQC"{ 
        }

        visual {

            fastqc {

                pos:"-493 -559";

                pos:"-480 -540";

                style:ext;

                bg-color-ext:"0 128 64 64";

                in-file.angle:180;

            }

            get-file-list {

                pos:"-773 -560";

                pos:"-765 -540";

                style:ext;

                bg-color-ext:"216 113 57 64";

                bounds:"-30 -30 116.25 84";
@@ -59,7 +58,6 @@ workflow "Quality control by FastQC"{ 
        }

        wizard {

            name:"Quality Control by FastQC Wizard";

            help-page-id:16122729;

            auto-run:true;

            page {

                id:1;

data/workflow_samples/NGS/from_tools_menu_only/ngs_classification.uwl

+2 −2
Original line number Diff line number Diff line
@@ -32,7 +32,7 @@ workflow "NGS reads classification" { 
                            value {

                                id: parallel;

                                label: "Parallel reads classification";

                                tooltip:"Improve reads quality with Trimmomatic, classify them with Kraken, CLARK and in case of single-end reads with DIAMOND. Join the classification output with WEVOTE.";

                                tooltip:"Improve reads quality with Trimmomatic, classify them with Kraken, CLARK, DIAMOND (in case of single-end reads), and MetaPhlAn2. Compare output from Kraken, CLARK, and DIAMOND with WEVOTE.";

                            }

                            value {

                                id: de_novo;