1 /**
2 * UGENE - Integrated Bioinformatics Tools.
3 * Copyright (C) 2008-2021 UniPro <ugene@unipro.ru>
4 * http://ugene.net
5 *
6 * This program is free software; you can redistribute it and/or
7 * modify it under the terms of the GNU General Public License
8 * as published by the Free Software Foundation; either version 2
9 * of the License, or (at your option) any later version.
10 *
11 * This program is distributed in the hope that it will be useful,
12 * but WITHOUT ANY WARRANTY; without even the implied warranty of
13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 * GNU General Public License for more details.
15 *
16 * You should have received a copy of the GNU General Public License
17 * along with this program; if not, write to the Free Software
18 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
19 * MA 02110-1301, USA.
20 */
21
22 #include "BowtieSupport.h"
23
24 #include <U2Core/AppContext.h>
25
26 namespace U2 {
27
28 // BowtieSupport
29 const QString BowtieSupport::ET_BOWTIE_ID = "USUPP_BOWTIE";
30 const QString BowtieSupport::ET_BOWTIE_BUILD_ID = "USUPP_BOWTIE_BUILD";
31
getBowtieToolNameById(const QString & id)32 static QString getBowtieToolNameById(const QString &id) {
33 return id == BowtieSupport::ET_BOWTIE_ID ? "Bowtie aligner" : "Bowtie build indexer";
34 }
35
BowtieSupport(const QString & id)36 BowtieSupport::BowtieSupport(const QString &id)
37 : ExternalTool(id, "bowtie1", getBowtieToolNameById(id)) {
38 if (AppContext::getMainWindow() != nullptr) {
39 icon = QIcon(":external_tool_support/images/cmdline.png");
40 grayIcon = QIcon(":external_tool_support/images/cmdline_gray.png");
41 warnIcon = QIcon(":external_tool_support/images/cmdline_warn.png");
42 }
43 if (id == ET_BOWTIE_ID) {
44 #ifdef Q_OS_WIN
45 executableFileName = "bowtie-align-s.exe";
46 #else
47 executableFileName = "bowtie-align-s";
48 #endif
49 } else {
50 #ifdef Q_OS_WIN
51 executableFileName = "bowtie-build-s.exe";
52 #else
53 executableFileName = "bowtie-build-s";
54 #endif
55 }
56 validationArguments.append("--version");
57 validMessage = "version";
58 description = tr("<i>Bowtie</i> is an ultrafast, memory-efficient short read aligner. "
59 "It aligns short DNA sequences (reads) to the human genome at "
60 "a rate of over 25 million 35-bp reads per hour. "
61 "Bowtie indexes the genome with a Burrows-Wheeler index to keep "
62 "its memory footprint small: typically about 2.2 GB for the human "
63 "genome (2.9 GB for paired-end).");
64 versionRegExp = QRegExp("version (\\d+\\.\\d+\\.\\d+)");
65 toolKitName = "Bowtie";
66 }
67
68 } // namespace U2
69
