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.gitignore
View file @ 373667d8
......@@ -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
\ No newline at end of file
.gitmodules
View file @ 373667d8
......@@ -2,3 +2,4 @@
path = src/libs_3rdparty/QSpec
url = https://github.com/ugeneunipro/QSpec.git
branch = ugene
ignore = dirty
\ No newline at end of file
.travis.yml
View file @ 373667d8
......@@ -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
......
CMakeLists.txt
View file @ 373667d8
......@@ -5,18 +5,18 @@
# * add Qt5_DIR variable to File->Settings->Build,Execution,Deployment->CMake pointing to valid QT dir.
# * add UGENE_TRANSLATION_FILE environment variable to the RUN configuration and point it to *.qm file produced by qmake build
cmake_minimum_required(VERSION 3.4)
cmake_minimum_required(VERSION 3.9)
project(ugene)
#set(CMAKE_VERBOSE_MAKEFILE ON)
set(UGENE_VERSION 1.25.0-dev)
set(UGENE_VERSION 1.29.0-dev)
set(UGENE_VER_MAJOR 1)
set(UGENE_VER_MINOR 25)
set(UGENE_VER_MINOR 29)
set(UGENE_VER_PATCH 0)
set(UGENE_MIN_VERSION_SQLITE 1.13.0)
set(UGENE_MIN_VERSION_MYSQL 1.16.0)
set(UGENE_MIN_VERSION_SQLITE 1.25.0)
set(UGENE_MIN_VERSION_MYSQL 1.25.0)
add_definitions(
-DUGENE_VERSION=${UGENE_VERSION}
......
README.md
View file @ 373667d8
......@@ -6,14 +6,12 @@
Make sure the Qt (>= 5.2.1 and < 5.6) development libraries are installed:
* Ubuntu 16.04: `sudo apt-get install qt5-default qttools5-dev-tools qtscript5-dev libqt5svg5-dev libqt5webkit5-dev libprocps4-dev`
* Ubuntu 14.04: `sudo apt-get install qt5-default qttools5-dev-tools qtscript5-dev libqt5svg5-dev libqt5webkit5-dev libprocps3-dev`
* Ubuntu >=14.04: `sudo apt-get install qt5-default qttools5-dev-tools qtscript5-dev libqt5svg5-dev libqt5webkit5-dev`
* Ubuntu 12.04:
* Download and install Qt 5.5.1: www.qt.io/download-open-source/
* Set the system variable: export PATH=$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/)
......
build.txt
View file @ 373667d8
......@@ -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/)
......
data/DBXRefRegistry.txt
View file @ 373667d8
......@@ -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.
......
data/adapters/illumina/NexteraPE-PE.fa 0 → 100644
View file @ 373667d8
>PrefixNX/1
AGATGTGTATAAGAGACAG
>PrefixNX/2
AGATGTGTATAAGAGACAG
>Trans1
TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
>Trans1_rc
CTGTCTCTTATACACATCTGACGCTGCCGACGA
>Trans2
GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
>Trans2_rc
CTGTCTCTTATACACATCTCCGAGCCCACGAGAC
\ No newline at end of file
data/adapters/illumina/TruSeq2-PE.fa 0 → 100644
View file @ 373667d8
>PrefixPE/1
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
>PrefixPE/2
CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
>PCR_Primer1
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
>PCR_Primer1_rc
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
>PCR_Primer2
CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
>PCR_Primer2_rc
AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG
>FlowCell1
TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC
>FlowCell2
TTTTTTTTTTCAAGCAGAAGACGGCATACGA
\ No newline at end of file
data/adapters/illumina/TruSeq2-SE.fa 0 → 100644
View file @ 373667d8
>TruSeq2_SE
AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
>TruSeq2_PE_f
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
>TruSeq2_PE_r
AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
\ No newline at end of file
data/adapters/illumina/TruSeq3-PE-2.fa 0 → 100644
View file @ 373667d8
>PrefixPE/1
TACACTCTTTCCCTACACGACGCTCTTCCGATCT
>PrefixPE/2
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
>PE1
TACACTCTTTCCCTACACGACGCTCTTCCGATCT
>PE1_rc
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
>PE2
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
>PE2_rc
AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
\ No newline at end of file
data/adapters/illumina/TruSeq3-PE.fa 0 → 100644
View file @ 373667d8
>PrefixPE/1
TACACTCTTTCCCTACACGACGCTCTTCCGATCT
>PrefixPE/2
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
\ No newline at end of file
data/adapters/illumina/TruSeq3-SE.fa 0 → 100644
View file @ 373667d8
>TruSeq3_IndexedAdapter
AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
>TruSeq3_UniversalAdapter
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
\ No newline at end of file
data/workflow_samples/Alignment/basic_align.uwl
View file @ 373667d8
......@@ -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;
......
data/workflow_samples/Alignment/extract_msa_consensus_as_seq.uwl
View file @ 373667d8
......@@ -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;
......
data/workflow_samples/Alignment/extract_msa_consensus_as_text.uwl
View file @ 373667d8
......@@ -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;
......
data/workflow_samples/Conversions/faqual2fastq.uwl
View file @ 373667d8
......@@ -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;
......
data/workflow_samples/Conversions/msa2clustal.uwl
View file @ 373667d8
......@@ -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;
......
data/workflow_samples/Conversions/query2alignment.uwl
View file @ 373667d8
......@@ -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;
......
data/workflow_samples/Conversions/seq2gen.uwl
View file @ 373667d8
......@@ -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;
......