Index: head/biology/ugene/Makefile
===================================================================
--- head/biology/ugene/Makefile (revision 478817)
+++ head/biology/ugene/Makefile (revision 478818)
@@ -1,78 +1,71 @@
# Created by: Hannes Hauswedell
# $FreeBSD$
PORTNAME= ugene
-DISTVERSION= 1.22.0
-PORTREVISION= 3
+DISTVERSION= 1.31.0
CATEGORIES= biology science
MASTER_SITES= http://ugene.unipro.ru/downloads/
DISTFILES= ${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \
UniproUGENE_UserManual.pdf WorkflowDesigner_UserManual.pdf
DIST_SUBDIR= ${PORTNAME}
EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX}
MAINTAINER= h2+fbsdports@fsfe.org
COMMENT= Free, open-source, cross-platform bioinformatics toolkit
-LICENSE= GPLv2
+LICENSE= GPLv2+
+LICENSE_FILE= ${WRKSRC}/LICENSE.txt
RUN_DEPENDS= bash:shells/bash
BROKEN_aarch64= Fails to build: invokes x86 asm
-USES= desktop-file-utils qmake qt:5
-USE_GL= glu
-USE_QT= buildtools_build linguisttools_build scripttools_build \
- gui network printsupport script sql svg webkit widgets xml \
+USES= desktop-file-utils qmake qt:5 shared-mime-info
+USE_GL= gl glu
+USE_QT= buildtools_build linguisttools_build \
+ core gui network opengl printsupport script scripttools \
+ sql svg testlib webkit widgets xml \
imageformats_run
+USE_XORG= x11 xtst
QMAKE_ARGS= INSTALL_PREFIX="${PREFIX}" UGENE_INSTALL_DATA="${DATADIR}" \
INSTALL_MANDIR="${MAN1PREFIX}/man" LRELEASE="${LRELEASE}" \
LUPDATE="${LUPDATE}"
ALL_TARGET= release
-# Required for Google Test code
-CXXFLAGS+= -std=c++11
-
DOCSDIR= ${DATADIR}/manuals
-OPTIONS_DEFINE= DOCS
+OPTIONS_DEFINE= DOCS OPENCL
DOCS_DESC= Install official UGENE documentation (PDF)
+OPENCL_QMAKE_ON= UGENE_OPENCL_DETECTED=1
+
.include
.if ${ARCH} == amd64
# XXX: need to manually tell the build we are on x64
QMAKE_ARGS+= CONFIG+=x64
-PLIST_SUB+= NOX64="@comment "
-.else
-PLIST_SUB+= NOX64=""
.endif
.if ${MACHINE_CPU:Msse2}
QMAKE_ARGS+= UGENE_SSE2_DETECTED=1
-PLIST_SUB+= SSE2=""
-.else
-PLIST_SUB+= SSE2="@comment "
.endif
post-extract:
@${MKDIR} ${WRKSRC}/data/manuals
${CP} -p ${_DISTDIR}/*.pdf ${WRKSRC}/data/manuals
post-patch:
# yes, bash is required, stuff will not execute with sh
@${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \
${WRKSRC}/src/gen_bin_script.cmd \
${WRKSRC}/installer/_common_data/ugene
@${REINPLACE_CMD} -e 's|-bit version|& for ${OPSYS}/${ARCH}|' \
${WRKSRC}/src/ugeneui/src/main_window/AboutDialogController.cpp
- @${REINPLACE_CMD} -e '/unix_not_mac/,+11d' \
- ${WRKSRC}/src/corelibs/U2Core/U2Core.pri
@${REINPLACE_CMD} 's, -lbreakpad,,' \
${WRKSRC}/src/corelibs/U2Private/U2Private.pri \
${WRKSRC}/src/plugins_checker/plugins_checker.pri \
${WRKSRC}/src/ugenecl/ugenecl.pri \
${WRKSRC}/src/ugeneui/ugeneui.pri
.include
Index: head/biology/ugene/distinfo
===================================================================
--- head/biology/ugene/distinfo (revision 478817)
+++ head/biology/ugene/distinfo (revision 478818)
@@ -1,8 +1,9 @@
-SHA256 (ugene/ugene-1.22.0.tar.gz) = ee46be799c9f02a9b6a89f13747a4918d5c96c01676dc2d4cc4a4c98278912b6
-SIZE (ugene/ugene-1.22.0.tar.gz) = 20986853
+TIMESTAMP = 1535840965
+SHA256 (ugene/ugene-1.31.0.tar.gz) = d1f46306834a292618cc54b31060b69da5b0b18da311a55bf82ab42f5a434320
+SIZE (ugene/ugene-1.31.0.tar.gz) = 20656562
SHA256 (ugene/QueryDesigner_UserManual.pdf) = 5d232c0de7e9d1fd32b8ee0a78f9f4abe1ab9d6536ec3958c47de29f3096faf4
SIZE (ugene/QueryDesigner_UserManual.pdf) = 855662
SHA256 (ugene/UniproUGENE_UserManual.pdf) = ae6aef32a6e92a30ba7c36cdd894a8caf634d678f15da7ad9eab52b6f40b9ed6
SIZE (ugene/UniproUGENE_UserManual.pdf) = 13443754
SHA256 (ugene/WorkflowDesigner_UserManual.pdf) = 8cc6630f62c82de42926c14c3d01ebc3c7d85ab7d9ec2a81e55a19740806735c
SIZE (ugene/WorkflowDesigner_UserManual.pdf) = 29474484
Index: head/biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h
===================================================================
--- head/biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h (revision 478817)
+++ head/biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h (nonexistent)
@@ -1,10 +0,0 @@
---- src/plugins_3rdparty/phylip/src/phylip.h.orig 2017-12-30 19:54:56 UTC
-+++ src/plugins_3rdparty/phylip/src/phylip.h
-@@ -271,7 +271,6 @@ MALLOCRETURN *mymalloc(long);
- #define MAXNCH 30 /* must be greater than or equal to nmlngth */
- #define maxcategs 9 /* maximum number of site types */
- #define maxcategs2 11 /* maximum number of site types + 2 */
--#define point "."
- #define pointe '.'
- #define down 2
- #define MAXSHIMOTREES 100
Property changes on: head/biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h
___________________________________________________________________
Deleted: fbsd:nokeywords
## -1 +0,0 ##
-yes
\ No newline at end of property
Deleted: svn:eol-style
## -1 +0,0 ##
-native
\ No newline at end of property
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property
Index: head/biology/ugene/files/patch-src_ugene__globals.pri
===================================================================
--- head/biology/ugene/files/patch-src_ugene__globals.pri (revision 478817)
+++ head/biology/ugene/files/patch-src_ugene__globals.pri (nonexistent)
@@ -1,13 +0,0 @@
---- src/ugene_globals.pri.orig 2016-03-31 12:22:21 UTC
-+++ src/ugene_globals.pri
-@@ -8,8 +8,8 @@ DEFINES+=UGENE_VER_MAJOR=$${UGENE_VER_MA
- DEFINES+=UGENE_VER_MINOR=$${UGENE_VER_MINOR}
- DEFINES+=UGENE_VER_PATCH=$${UGENE_VER_PATCH}
-
--unix : !macx : INCLUDEPATH-=/usr/include
--unix : !macx : INCLUDEPATH+=/usr/include/qt5 /usr/include
-+#unix : !macx : INCLUDEPATH-=/usr/include
-+#unix : !macx : INCLUDEPATH+=/usr/include/qt5 /usr/include
- #unix : !macx : INCLUDEPATH =/usr/include/qt5 $$INCLUDEPATH
-
- # NGS package
Property changes on: head/biology/ugene/files/patch-src_ugene__globals.pri
___________________________________________________________________
Deleted: fbsd:nokeywords
## -1 +0,0 ##
-yes
\ No newline at end of property
Deleted: svn:eol-style
## -1 +0,0 ##
-native
\ No newline at end of property
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property
Index: head/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri
===================================================================
--- head/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri (revision 478817)
+++ head/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri (nonexistent)
@@ -1,11 +0,0 @@
---- src/plugins_3rdparty/variants/variants.pri.orig 2016-03-31 12:22:09 UTC
-+++ src/plugins_3rdparty/variants/variants.pri
-@@ -20,7 +20,7 @@ use_bundled_zlib() {
- win32 : LIBS += -lwsock32
-
-
--INCLUDEPATH += src ../../include /usr/include
-+INCLUDEPATH += src ../../include
- INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools
- INCLUDEPATH += ../../libs_3rdparty/samtools/src
- INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools/bcftools
Property changes on: head/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri
___________________________________________________________________
Deleted: fbsd:nokeywords
## -1 +0,0 ##
-yes
\ No newline at end of property
Deleted: svn:eol-style
## -1 +0,0 ##
-native
\ No newline at end of property
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property
Index: head/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri
===================================================================
--- head/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri (revision 478817)
+++ head/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri (nonexistent)
@@ -1,11 +0,0 @@
---- src/libs_3rdparty/samtools/samtools.pri.orig 2016-03-31 12:21:56 UTC
-+++ src/libs_3rdparty/samtools/samtools.pri
-@@ -3,7 +3,7 @@ UGENE_RELATIVE_DESTDIR = ''
-
- TEMPLATE = lib
- CONFIG +=thread debug_and_release staticlib warn_off
--INCLUDEPATH += src src/samtools ../../include /usr/include
-+INCLUDEPATH += src src/samtools ../../include
- win32 : INCLUDEPATH += src/samtools/win32
- DEFINES+="_FILE_OFFSET_BITS=64" _LARGEFILE64_SOURCE _USE_KNETFILE
- win32 : DEFINES += _USE_MATH_DEFINES "inline=__inline" "__func__=__FUNCTION__" "R_OK=4" "atoll=_atoi64" "alloca=_alloca"
Property changes on: head/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri
___________________________________________________________________
Deleted: fbsd:nokeywords
## -1 +0,0 ##
-yes
\ No newline at end of property
Deleted: svn:eol-style
## -1 +0,0 ##
-native
\ No newline at end of property
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property
Index: head/biology/ugene/files/patch-git_279756e4
===================================================================
--- head/biology/ugene/files/patch-git_279756e4 (revision 478817)
+++ head/biology/ugene/files/patch-git_279756e4 (nonexistent)
@@ -1,30 +0,0 @@
-From 279756e448f53af5a495a2ce3a12abdf833fc703 Mon Sep 17 00:00:00 2001
-From: Kevin Kofler
-Date: Tue, 2 Jan 2018 22:21:03 +0100
-Subject: [PATCH] Fix build against Qt 5.10
-MIME-Version: 1.0
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-
-src/plugins/external_tool_support/src/bowtie2/Bowtie2Settings.ui: Remove
-shortcut setting that breaks the build with Qt 5.10.
-
-UGENE can be built with Qt ≥ 5.6 and a separate QtWebKit. With Qt 5.10,
-we were hitting a build error: uic was producing code that did not
-compile.
----
- src/plugins/external_tool_support/src/bowtie2/Bowtie2Settings.ui | 3 ---
- 1 file changed, 3 deletions(-)
-
---- src/plugins/external_tool_support/src/ui/Bowtie2Settings.ui
-+++ src/plugins/external_tool_support/src/ui/Bowtie2Settings.ui
-@@ -254,9 +254,6 @@
-
- Disallow gaps (--gbar)
-
--
--
--
-
-
-
Property changes on: head/biology/ugene/files/patch-git_279756e4
___________________________________________________________________
Deleted: fbsd:nokeywords
## -1 +0,0 ##
-yes
\ No newline at end of property
Deleted: svn:eol-style
## -1 +0,0 ##
-native
\ No newline at end of property
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property
Index: head/biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp
===================================================================
--- head/biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp (revision 478817)
+++ head/biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp (nonexistent)
@@ -1,14 +0,0 @@
---- src/plugins_3rdparty/umuscle/src/MuscleWorkPool.cpp.orig 2016-03-31 12:22:09 UTC
-+++ src/plugins_3rdparty/umuscle/src/MuscleWorkPool.cpp
-@@ -28,9 +28,10 @@ namespace U2 {
-
- MuscleWorkPool::MuscleWorkPool(MuscleContext *_ctx, const MuscleTaskSettings &_config, TaskStateInfo& _ti, int _nThreads, const MAlignment& _ma, MAlignment& _res, bool _mhack)
- :ctx(_ctx), config(_config), ma(_ma), res(_res), mhack(_mhack), Weights(NULL), ProgNodes(NULL), ph(NULL), ti(_ti),
-- treeNodeStatus(NULL), treeNodeIndexes(NULL), nThreads(_nThreads), uJoin(0), ptrbOscillating(false), bAnyAccepted(false), InternalNodeIndexes(NULL), uInternalNodeCount(0),
-+ treeNodeStatus(NULL), treeNodeIndexes(NULL), nThreads(_nThreads), uJoin(0), bAnyAccepted(false), InternalNodeIndexes(NULL), uInternalNodeCount(0),
- bReversed(false), bRight(false), History(NULL), bLockLeft(NULL), bLockRight(false), msaIn(NULL)
- {
-+ *ptrbOscillating = false;
- refineConstructot();
- }
- MuscleWorkPool::~MuscleWorkPool() {
Property changes on: head/biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp
___________________________________________________________________
Deleted: fbsd:nokeywords
## -1 +0,0 ##
-yes
\ No newline at end of property
Deleted: svn:eol-style
## -1 +0,0 ##
-native
\ No newline at end of property
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property
Index: head/biology/ugene/files/patch-git_578c949
===================================================================
--- head/biology/ugene/files/patch-git_578c949 (nonexistent)
+++ head/biology/ugene/files/patch-git_578c949 (revision 478818)
@@ -0,0 +1,25 @@
+From 578c949ae7df017e23c3eda0293faa3db718c89f Mon Sep 17 00:00:00 2001
+From: Yuliya Algaer
+Date: Fri, 24 Aug 2018 21:24:12 +0700
+Subject: [PATCH] Build fix for Fedora
+
+--- src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp.orig 2018-08-16 13:58:58 UTC
++++ src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp
+@@ -20,6 +20,7 @@
+ */
+
+ #include
++#include
+
+ #include "LengthSettingsWidget.h"
+ #include "LineEditHighlighter.h"
+--- src/plugins/external_tool_support/src/trimmomatic/util/QualitySettingsWidget.cpp.orig 2018-08-16 13:58:58 UTC
++++ src/plugins/external_tool_support/src/trimmomatic/util/QualitySettingsWidget.cpp
+@@ -19,6 +19,7 @@
+ * MA 02110-1301, USA.
+ */
+
++#include
+ #include
+
+ #include "QualitySettingsWidget.h"
Property changes on: head/biology/ugene/files/patch-git_578c949
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: head/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro
===================================================================
--- head/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro (revision 478817)
+++ head/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro (revision 478818)
@@ -1,47 +1,41 @@
---- src/corelibs/U2Private/U2Private.pro.orig 2016-03-31 12:22:14 UTC
+--- src/corelibs/U2Private/U2Private.pro.orig 2018-08-16 13:59:12 UTC
+++ src/corelibs/U2Private/U2Private.pro
@@ -12,12 +12,7 @@ HEADERS += src/AppContextImpl.h \
src/PluginSupportImpl.h \
src/ServiceRegistryImpl.h \
src/SettingsImpl.h \
- src/TaskSchedulerImpl.h \
- src/crash_handler/CrashHandler.h \
- src/crash_handler/CrashHandlerArgsHelper.h \
- src/crash_handler/CrashHandlerPrivate.h \
- src/crash_handler/CrashLogCache.h \
- src/crash_handler/StackWalker.h
+ src/TaskSchedulerImpl.h
SOURCES += src/AppContextImpl.cpp \
src/AppSettingsImpl.cpp \
-@@ -30,29 +25,7 @@ SOURCES += src/AppContextImpl.cpp \
+@@ -30,23 +25,13 @@ SOURCES += src/AppContextImpl.cpp \
src/PluginSupportImpl.cpp \
src/ServiceRegistryImpl.cpp \
src/SettingsImpl.cpp \
- src/TaskSchedulerImpl.cpp \
- src/crash_handler/CrashHandler.cpp \
- src/crash_handler/CrashHandlerArgsHelper.cpp \
- src/crash_handler/CrashHandlerPrivate.cpp \
- src/crash_handler/CrashLogCache.cpp \
- src/crash_handler/StackWalker.cpp
+ src/TaskSchedulerImpl.cpp
- TRANSLATIONS += transl/english.ts \
- transl/russian.ts
--
--win32 {
-- HEADERS += src/crash_handler/CrashHandlerPrivateWin.h
-- SOURCES += src/crash_handler/CrashHandlerPrivateWin.cpp
+ TRANSLATIONS += transl/russian.ts
+
+ win32 {
+ HEADERS += src/crash_handler/CrashHandlerPrivateWin.h
+ SOURCES += src/crash_handler/CrashHandlerPrivateWin.cpp
-}
-
-unix_not_mac() {
- HEADERS += src/crash_handler/CrashHandlerPrivateUnixNotMac.h
- SOURCES += src/crash_handler/CrashHandlerPrivateUnixNotMac.cpp
--}
--
--mac {
-- HEADERS += src/crash_handler/CrashHandlerPrivateMac.h \
-- src/SleepPreventerMac.h
-- SOURCES += src/crash_handler/CrashHandlerPrivateMac.cpp \
-- src/SleepPreventerMac.cpp
--}
+ }
+
+ mac {
Index: head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp
===================================================================
--- head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp (nonexistent)
+++ head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp (revision 478818)
@@ -0,0 +1,22 @@
+Use the Linux driver for FreeBSD as well. Fixes crash on startup.
+
+--- src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp.orig 2018-09-02 00:22:54 UTC
++++ src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp
+@@ -22,7 +22,7 @@
+ #include
+ #include "GTKeyboardDriver.h"
+
+-#if defined __linux__
++#if defined(__linux__) || defined(__FreeBSD__)
+ #define XK_LATIN1 // for latin symbol
+ #define XK_MISCELLANY // for action keys
+ #include
+@@ -31,7 +31,7 @@
+
+ namespace HI {
+
+-#if defined __linux__
++#if defined(__linux__) || defined(__FreeBSD__)
+
+ #define GT_CLASS_NAME "GTKeyboardDriverLinux"
+
Property changes on: head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp
===================================================================
--- head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp (nonexistent)
+++ head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp (revision 478818)
@@ -0,0 +1,20 @@
+Use the Linux driver for FreeBSD as well. Fixes crash on startup.
+
+--- src/libs_3rdparty/QSpec/src/drivers/GTMouseDriverLinux.cpp.orig 2018-09-02 00:23:24 UTC
++++ src/libs_3rdparty/QSpec/src/drivers/GTMouseDriverLinux.cpp
+@@ -22,13 +22,13 @@
+ #include "GTMouseDriver.h"
+ #include
+
+-#ifdef __linux__
++#if defined(__linux__) || defined(__FreeBSD__)
+ #include
+ #endif
+
+ namespace HI {
+
+-#ifdef __linux__
++#if defined(__linux__) || defined(__FreeBSD__)
+
+ #define GT_CLASS_NAME "GTMouseDriver Linux"
+ QPoint GTMouseDriver::mousePos = QPoint(-1, -1);
Property changes on: head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: head/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp
===================================================================
--- head/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp (revision 478817)
+++ head/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp (revision 478818)
@@ -1,31 +1,31 @@
---- src/plugins_checker/src/Main.cpp.orig 2016-03-31 12:22:09 UTC
+--- src/plugins_checker/src/Main.cpp.orig 2018-08-16 13:59:06 UTC
+++ src/plugins_checker/src/Main.cpp
@@ -39,7 +39,7 @@
#include
#include
#include
-#include
+//#include
#define TR_SETTINGS_ROOT QString("test_runner/")
@@ -55,8 +55,10 @@ static void registerCoreServices() {
int main(int argc, char **argv)
{
+#if 0
CrashHandler::setupHandler();
CrashHandler::setSendCrashReports(false);
+#endif
const char* build = QT_VERSION_STR, *runtime = qVersion();
if (strcmp(build, runtime) > 0){
-@@ -140,7 +142,7 @@ int main(int argc, char **argv)
+@@ -141,7 +143,7 @@ int main(int argc, char **argv)
delete cmdLineRegistry;
appContext->setCMDLineRegistry(NULL);
- CrashHandler::shutdown();
+ //CrashHandler::shutdown();
return rc;
}
Index: head/biology/ugene/files/patch-src_ugenecl_src_Main.cpp
===================================================================
--- head/biology/ugene/files/patch-src_ugenecl_src_Main.cpp (revision 478817)
+++ head/biology/ugene/files/patch-src_ugenecl_src_Main.cpp (revision 478818)
@@ -1,32 +1,36 @@
---- src/ugenecl/src/Main.cpp.orig 2016-03-31 12:22:19 UTC
+--- src/ugenecl/src/Main.cpp.orig 2018-08-16 13:59:20 UTC
+++ src/ugenecl/src/Main.cpp
-@@ -94,7 +94,7 @@
+@@ -93,7 +93,7 @@
#include
#include
#include
-#include
+//#include
// local project imports
#include "DumpHelpTask.h"
-@@ -192,9 +192,11 @@ static void setSearchPaths() {
+@@ -191,6 +191,7 @@ static void setSearchPaths() {
int main(int argc, char **argv)
{
+#if 0
if (CrashHandler::isEnabled()) {
CrashHandler::setupHandler();
}
+@@ -198,6 +199,7 @@ int main(int argc, char **argv)
+ if (qgetenv(ENV_SEND_CRASH_REPORTS) == "0") {
+ CrashHandler::setSendCrashReports(false);
+ }
+#endif
+
const char* build = QT_VERSION_STR, *runtime = qVersion();
if (strcmp(build, runtime) > 0){
- printf("Installed Qt version must be %s or greater \r\n", QT_VERSION_STR);
@@ -617,7 +619,7 @@ int main(int argc, char **argv)
delete pwr;
appContext->setAlignmentAlgorithmsRegistry(NULL);
- CrashHandler::shutdown();
+ //CrashHandler::shutdown();
return rc;
}
Index: head/biology/ugene/files/patch-src_ugeneui_src_Main.cpp
===================================================================
--- head/biology/ugene/files/patch-src_ugeneui_src_Main.cpp (revision 478817)
+++ head/biology/ugene/files/patch-src_ugeneui_src_Main.cpp (revision 478818)
@@ -1,32 +1,36 @@
---- src/ugeneui/src/Main.cpp.orig 2016-03-31 12:22:18 UTC
+--- src/ugeneui/src/Main.cpp.orig 2018-08-16 13:59:19 UTC
+++ src/ugeneui/src/Main.cpp
-@@ -134,7 +134,7 @@
+@@ -136,7 +136,7 @@
#include
#include
#include
-#include
+//#include
#include "app_settings/AppSettingsGUIImpl.h"
#include "app_settings/logview_settings/LogSettingsGUIController.h"
-@@ -343,9 +343,11 @@ void fixMacFonts() {
+@@ -353,6 +353,7 @@ void fixMacFonts() {
int main(int argc, char **argv)
{
+#if 0
if (CrashHandler::isEnabled()) {
CrashHandler::setupHandler();
}
+@@ -360,6 +361,7 @@ int main(int argc, char **argv)
+ if (qgetenv(ENV_SEND_CRASH_REPORTS) == "0") {
+ CrashHandler::setSendCrashReports(false);
+ }
+#endif
QT_REQUIRE_VERSION( argc, argv, QT_VERSION_STR );
-@@ -966,7 +968,7 @@ int main(int argc, char **argv)
+@@ -973,7 +975,7 @@ int main(int argc, char **argv)
}
UgeneUpdater::onClose();
- CrashHandler::shutdown();
+ //CrashHandler::shutdown();
return rc;
}
Index: head/biology/ugene/files/patch-ugene.pro
===================================================================
--- head/biology/ugene/files/patch-ugene.pro (revision 478817)
+++ head/biology/ugene/files/patch-ugene.pro (revision 478818)
@@ -1,28 +1,29 @@
---- ugene.pro.orig 2016-03-31 12:21:56 UTC
+--- ugene.pro.orig 2018-08-16 13:58:51 UTC
+++ ugene.pro
@@ -20,7 +20,6 @@ use_bundled_zlib() {
}
SUBDIRS += \
- src/libs_3rdparty/breakpad \
src/libs_3rdparty/qscore \
src/libs_3rdparty/sqlite3 \
- src/libs_3rdparty/gtest \
-@@ -144,15 +143,8 @@ UGENE_TRANSL_QM_TARGET_DIR = $$OUT_PWD/s
+ src/libs_3rdparty/samtools \
+@@ -141,16 +140,8 @@ UGENE_TRANSL_QM_TARGET_DIR = $$OUT_PWD/src/_debug $$OU
win32 : UGENE_DEV_NULL = nul
unix : UGENE_DEV_NULL = /dev/null
-UGENE_LRELEASE =
--UGENE_LUPDATE =
--system(lrelease-qt5 -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
-- UGENE_LRELEASE = lrelease-qt5
-- UGENE_LUPDATE = lupdate-qt5
--} else : system(lrelease -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
-- UGENE_LRELEASE = lrelease
-- UGENE_LUPDATE = lupdate
+-UGENE_LUPDATE =
+-message(Using QT from $$[QT_INSTALL_BINS])
+-system($$[QT_INSTALL_BINS]/lrelease-qt5 -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
+- UGENE_LRELEASE = $$[QT_INSTALL_BINS]/lrelease-qt5
+- UGENE_LUPDATE = $$[QT_INSTALL_BINS]/lupdate-qt5
+-} else : system($$[QT_INSTALL_BINS]/lrelease -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
+- UGENE_LRELEASE = $$[QT_INSTALL_BINS]/lrelease
+- UGENE_LUPDATE = $$[QT_INSTALL_BINS]/lupdate
-}
+UGENE_LRELEASE = $$LRELEASE
+UGENE_LUPDATE = $$LUPDATE
#foreach 'language'
for( i, UGENE_TRANSL_IDX ) {
Index: head/biology/ugene/pkg-plist
===================================================================
--- head/biology/ugene/pkg-plist (revision 478817)
+++ head/biology/ugene/pkg-plist (revision 478818)
@@ -1,1447 +1,1492 @@
bin/ugene
+lib/ugene/libQSpec.so
+lib/ugene/libQSpec.so.1
+lib/ugene/libQSpec.so.1.0
+lib/ugene/libQSpec.so.1.0.0
lib/ugene/libU2Algorithm.so
lib/ugene/libU2Algorithm.so.1
lib/ugene/libU2Algorithm.so.1.0
lib/ugene/libU2Algorithm.so.1.0.0
lib/ugene/libU2Core.so
lib/ugene/libU2Core.so.1
lib/ugene/libU2Core.so.1.0
lib/ugene/libU2Core.so.1.0.0
lib/ugene/libU2Designer.so
lib/ugene/libU2Designer.so.1
lib/ugene/libU2Designer.so.1.0
lib/ugene/libU2Designer.so.1.0.0
lib/ugene/libU2Formats.so
lib/ugene/libU2Formats.so.1
lib/ugene/libU2Formats.so.1.0
lib/ugene/libU2Formats.so.1.0.0
lib/ugene/libU2Gui.so
lib/ugene/libU2Gui.so.1
lib/ugene/libU2Gui.so.1.0
lib/ugene/libU2Gui.so.1.0.0
lib/ugene/libU2Lang.so
lib/ugene/libU2Lang.so.1
lib/ugene/libU2Lang.so.1.0
lib/ugene/libU2Lang.so.1.0.0
lib/ugene/libU2Private.so
lib/ugene/libU2Private.so.1
lib/ugene/libU2Private.so.1.0
lib/ugene/libU2Private.so.1.0.0
-lib/ugene/libU2Remote.so
-lib/ugene/libU2Remote.so.1
-lib/ugene/libU2Remote.so.1.0
-lib/ugene/libU2Remote.so.1.0.0
lib/ugene/libU2Script.so
lib/ugene/libU2Script.so.1
lib/ugene/libU2Script.so.1.0
lib/ugene/libU2Script.so.1.0.0
lib/ugene/libU2Test.so
lib/ugene/libU2Test.so.1
lib/ugene/libU2Test.so.1.0
lib/ugene/libU2Test.so.1.0.0
lib/ugene/libU2View.so
lib/ugene/libU2View.so.1
lib/ugene/libU2View.so.1.0
lib/ugene/libU2View.so.1.0.0
-lib/ugene/libgtest.so
-lib/ugene/libgtest.so.1
-lib/ugene/libgtest.so.1.0
-lib/ugene/libgtest.so.1.0.0
lib/ugene/libugenedb.so
lib/ugene/libugenedb.so.1
lib/ugene/libugenedb.so.1.0
lib/ugene/libugenedb.so.1.0.0
lib/ugene/plugins/CoreTests.license
lib/ugene/plugins/CoreTests.plugin
+lib/ugene/plugins/GUITestBase.license
+lib/ugene/plugins/GUITestBase.plugin
lib/ugene/plugins/annotator.license
lib/ugene/plugins/annotator.plugin
lib/ugene/plugins/api_tests.license
lib/ugene/plugins/api_tests.plugin
lib/ugene/plugins/ball.license
lib/ugene/plugins/ball.plugin
lib/ugene/plugins/biostruct3d_view.license
lib/ugene/plugins/biostruct3d_view.plugin
lib/ugene/plugins/browser_support.license
lib/ugene/plugins/browser_support.plugin
lib/ugene/plugins/chroma_view.license
lib/ugene/plugins/chroma_view.plugin
lib/ugene/plugins/circular_view.license
lib/ugene/plugins/circular_view.plugin
+lib/ugene/plugins/clark_support.license
+lib/ugene/plugins/clark_support.plugin
lib/ugene/plugins/dbi_bam.license
lib/ugene/plugins/dbi_bam.plugin
+lib/ugene/plugins/diamond_support.license
+lib/ugene/plugins/diamond_support.plugin
lib/ugene/plugins/dna_export.license
lib/ugene/plugins/dna_export.plugin
lib/ugene/plugins/dna_flexibility.license
lib/ugene/plugins/dna_flexibility.plugin
lib/ugene/plugins/dna_graphpack.license
lib/ugene/plugins/dna_graphpack.plugin
lib/ugene/plugins/dna_stat.license
lib/ugene/plugins/dna_stat.plugin
lib/ugene/plugins/dotplot.license
lib/ugene/plugins/dotplot.plugin
lib/ugene/plugins/enzymes.license
lib/ugene/plugins/enzymes.plugin
lib/ugene/plugins/external_tool_support.license
lib/ugene/plugins/external_tool_support.plugin
lib/ugene/plugins/genome_aligner.license
lib/ugene/plugins/genome_aligner.plugin
lib/ugene/plugins/gor4.license
lib/ugene/plugins/gor4.plugin
lib/ugene/plugins/hmm2.license
lib/ugene/plugins/hmm2.plugin
-%%SSE2%%lib/ugene/plugins/hmm3.license
-%%SSE2%%lib/ugene/plugins/hmm3.plugin
lib/ugene/plugins/kalign.license
lib/ugene/plugins/kalign.plugin
+lib/ugene/plugins/kraken_support.license
+lib/ugene/plugins/kraken_support.plugin
lib/ugene/plugins/libCoreTests.so
lib/ugene/plugins/libCoreTests.so.1
lib/ugene/plugins/libCoreTests.so.1.0
lib/ugene/plugins/libCoreTests.so.1.0.0
+lib/ugene/plugins/libGUITestBase.so
+lib/ugene/plugins/libGUITestBase.so.1
+lib/ugene/plugins/libGUITestBase.so.1.0
+lib/ugene/plugins/libGUITestBase.so.1.0.0
lib/ugene/plugins/libannotator.so
lib/ugene/plugins/libannotator.so.1
lib/ugene/plugins/libannotator.so.1.0
lib/ugene/plugins/libannotator.so.1.0.0
lib/ugene/plugins/libapi_tests.so
lib/ugene/plugins/libapi_tests.so.1
lib/ugene/plugins/libapi_tests.so.1.0
lib/ugene/plugins/libapi_tests.so.1.0.0
lib/ugene/plugins/libball.so
lib/ugene/plugins/libball.so.1
lib/ugene/plugins/libball.so.1.0
lib/ugene/plugins/libball.so.1.0.0
lib/ugene/plugins/libbiostruct3d_view.so
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lib/ugene/plugins/libbiostruct3d_view.so.1.0
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lib/ugene/plugins/libbrowser_support.so
lib/ugene/plugins/libbrowser_support.so.1
lib/ugene/plugins/libbrowser_support.so.1.0
lib/ugene/plugins/libbrowser_support.so.1.0.0
lib/ugene/plugins/libchroma_view.so
lib/ugene/plugins/libchroma_view.so.1
lib/ugene/plugins/libchroma_view.so.1.0
lib/ugene/plugins/libchroma_view.so.1.0.0
lib/ugene/plugins/libcircular_view.so
lib/ugene/plugins/libcircular_view.so.1
lib/ugene/plugins/libcircular_view.so.1.0
lib/ugene/plugins/libcircular_view.so.1.0.0
+lib/ugene/plugins/libclark_support.so
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+lib/ugene/plugins/libclark_support.so.1.0.0
lib/ugene/plugins/libdbi_bam.so
lib/ugene/plugins/libdbi_bam.so.1
lib/ugene/plugins/libdbi_bam.so.1.0
lib/ugene/plugins/libdbi_bam.so.1.0.0
+lib/ugene/plugins/libdiamond_support.so
+lib/ugene/plugins/libdiamond_support.so.1
+lib/ugene/plugins/libdiamond_support.so.1.0
+lib/ugene/plugins/libdiamond_support.so.1.0.0
lib/ugene/plugins/libdna_export.so
lib/ugene/plugins/libdna_export.so.1
lib/ugene/plugins/libdna_export.so.1.0
lib/ugene/plugins/libdna_export.so.1.0.0
lib/ugene/plugins/libdna_flexibility.so
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lib/ugene/plugins/libdna_flexibility.so.1.0.0
lib/ugene/plugins/libdna_graphpack.so
lib/ugene/plugins/libdna_graphpack.so.1
lib/ugene/plugins/libdna_graphpack.so.1.0
lib/ugene/plugins/libdna_graphpack.so.1.0.0
lib/ugene/plugins/libdna_stat.so
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lib/ugene/plugins/libdotplot.so
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lib/ugene/plugins/libdotplot.so.1.0
lib/ugene/plugins/libdotplot.so.1.0.0
lib/ugene/plugins/libenzymes.so
lib/ugene/plugins/libenzymes.so.1
lib/ugene/plugins/libenzymes.so.1.0
lib/ugene/plugins/libenzymes.so.1.0.0
lib/ugene/plugins/libexternal_tool_support.so
lib/ugene/plugins/libexternal_tool_support.so.1
lib/ugene/plugins/libexternal_tool_support.so.1.0
lib/ugene/plugins/libexternal_tool_support.so.1.0.0
lib/ugene/plugins/libgenome_aligner.so
lib/ugene/plugins/libgenome_aligner.so.1
lib/ugene/plugins/libgenome_aligner.so.1.0
lib/ugene/plugins/libgenome_aligner.so.1.0.0
lib/ugene/plugins/libgor4.so
lib/ugene/plugins/libgor4.so.1
lib/ugene/plugins/libgor4.so.1.0
lib/ugene/plugins/libgor4.so.1.0.0
lib/ugene/plugins/libhmm2.so
lib/ugene/plugins/libhmm2.so.1
lib/ugene/plugins/libhmm2.so.1.0
lib/ugene/plugins/libhmm2.so.1.0.0
-%%SSE2%%lib/ugene/plugins/libhmm3.so
-%%SSE2%%lib/ugene/plugins/libhmm3.so.1
-%%SSE2%%lib/ugene/plugins/libhmm3.so.1.0
-%%SSE2%%lib/ugene/plugins/libhmm3.so.1.0.0
lib/ugene/plugins/libkalign.so
lib/ugene/plugins/libkalign.so.1
lib/ugene/plugins/libkalign.so.1.0
lib/ugene/plugins/libkalign.so.1.0.0
+lib/ugene/plugins/libkraken_support.so
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+lib/ugene/plugins/libkraken_support.so.1.0.0
lib/ugene/plugins/liblinkdata_support.so
lib/ugene/plugins/liblinkdata_support.so.1
lib/ugene/plugins/liblinkdata_support.so.1.0
lib/ugene/plugins/liblinkdata_support.so.1.0.0
+lib/ugene/plugins/libngs_reads_classification.so
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+lib/ugene/plugins/libngs_reads_classification.so.1.0.0
lib/ugene/plugins/libopencl_support.so
lib/ugene/plugins/libopencl_support.so.1
lib/ugene/plugins/libopencl_support.so.1.0
lib/ugene/plugins/libopencl_support.so.1.0.0
lib/ugene/plugins/liborf_marker.so
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lib/ugene/plugins/libphylip.so
lib/ugene/plugins/libphylip.so.1
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lib/ugene/plugins/libptools.so
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lib/ugene/plugins/libptools.so.1.0.0
lib/ugene/plugins/libquery_designer.so
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lib/ugene/plugins/libremote_blast.so.1
lib/ugene/plugins/libremote_blast.so.1.0
lib/ugene/plugins/libremote_blast.so.1.0.0
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lib/ugene/plugins/librepeat_finder.so
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lib/ugene/plugins/libvariants.so
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lib/ugene/plugins/libvariants.so.1.0
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lib/ugene/plugins/libweight_matrix.so
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lib/ugene/plugins/libweight_matrix.so.1.0.0
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lib/ugene/plugins/libworkflow_designer.so
lib/ugene/plugins/libworkflow_designer.so.1
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lib/ugene/plugins/libworkflow_designer.so.1.0.0
lib/ugene/plugins/linkdata_support.license
lib/ugene/plugins/linkdata_support.plugin
+lib/ugene/plugins/ngs_reads_classification.license
+lib/ugene/plugins/ngs_reads_classification.plugin
lib/ugene/plugins/opencl_support.license
lib/ugene/plugins/opencl_support.plugin
lib/ugene/plugins/orf_marker.license
lib/ugene/plugins/orf_marker.plugin
lib/ugene/plugins/pcr.license
lib/ugene/plugins/pcr.plugin
lib/ugene/plugins/perf_monitor.license
lib/ugene/plugins/perf_monitor.plugin
lib/ugene/plugins/phylip.license
lib/ugene/plugins/phylip.plugin
lib/ugene/plugins/primer3.license
lib/ugene/plugins/primer3.plugin
lib/ugene/plugins/psipred.license
lib/ugene/plugins/psipred.plugin
lib/ugene/plugins/ptools.license
lib/ugene/plugins/ptools.plugin
lib/ugene/plugins/query_designer.license
lib/ugene/plugins/query_designer.plugin
lib/ugene/plugins/remote_blast.license
lib/ugene/plugins/remote_blast.plugin
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lib/ugene/plugins/repeat_finder.license
lib/ugene/plugins/repeat_finder.plugin
lib/ugene/plugins/sitecon.license
lib/ugene/plugins/sitecon.plugin
lib/ugene/plugins/smith_waterman.license
lib/ugene/plugins/smith_waterman.plugin
lib/ugene/plugins/test_runner.license
lib/ugene/plugins/test_runner.plugin
-%%NOX64%%lib/ugene/plugins/umuscle.license
-%%NOX64%%lib/ugene/plugins/umuscle.plugin
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lib/ugene/plugins/variants.license
lib/ugene/plugins/variants.plugin
lib/ugene/plugins/weight_matrix.license
lib/ugene/plugins/weight_matrix.plugin
+lib/ugene/plugins/wevote_support.license
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lib/ugene/plugins/workflow_designer.license
lib/ugene/plugins/workflow_designer.plugin
lib/ugene/plugins_checker
lib/ugene/transl_en.qm
lib/ugene/transl_ru.qm
lib/ugene/ugene
lib/ugene/ugenecl
lib/ugene/ugenem
lib/ugene/ugeneui
man/man1/ugene.1.gz
share/applications/ugene.desktop
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+share/mime/packages/application-x-ugene.xml
share/pixmaps/ugene.png
share/pixmaps/ugene.xpm
%%DATADIR%%/DBXRefRegistry.txt
%%DATADIR%%/adapters/adapters.fasta
+%%DATADIR%%/adapters/illumina/NexteraPE-PE.fa
+%%DATADIR%%/adapters/illumina/TruSeq2-PE.fa
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%%DATADIR%%/back_translation/Bacteria/Arthrobacter_aurescens_TC1.cut
%%DATADIR%%/back_translation/Bacteria/Bacillus_subtilis.cut
%%DATADIR%%/back_translation/Bacteria/Escherichia_coli.cut
%%DATADIR%%/back_translation/Bacteria/Haemophilus_influenzae.cut
%%DATADIR%%/back_translation/Bacteria/Helicobacter_pylori.cut
%%DATADIR%%/back_translation/Bacteria/Listeria_monocytogenes.cut
%%DATADIR%%/back_translation/Bacteria/Neisseria_meningitidis.cut
%%DATADIR%%/back_translation/Bacteria/Salmonella_typhimurium_LT2.cut
%%DATADIR%%/back_translation/Bacteria/Streptomyces_coelicolor_A3(2).cut
%%DATADIR%%/back_translation/Bacteria/Sulfolobus_solfataricus_P2.cut
%%DATADIR%%/back_translation/Invertebrates/Apis_mellifera_(honey_bee).cut
%%DATADIR%%/back_translation/Invertebrates/Caenorhabditis_elegans.cut
%%DATADIR%%/back_translation/Invertebrates/Drosophila_melanogaster_(fruit_fly).cut
%%DATADIR%%/back_translation/Invertebrates/Plasmodium_falciparum_(malaria_parasite_P._falciparum).cut
%%DATADIR%%/back_translation/Invertebrates/mitochondrion_Caenorhabditis_elegans.cut
%%DATADIR%%/back_translation/Invertebrates/mitochondrion_Drosophila_melanogaster_(fruit_fly).cut
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%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Gsh2_3990.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hdx_3845.3.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hlx1_2350.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hlxb9_3422.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hmbox1_2674.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hmx1_3423.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hmx2_3424.3.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hmx3_3490.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Homez_1063.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa10_2318.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa11_2218.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa13_3126.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa1_3425.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa2_3079.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa3_2783.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa4_3426.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa5_3415.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa6_1040.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa7_2668.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa7_3750.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa9_2622.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb13_3479.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb3_1720.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb4_2627.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb5_3122.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb6_3428.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb7_3953.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb8_3780.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb9_3413.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc10_2779.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc11_3718.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc12_3480.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc13_3127.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc4_3491.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc5_2630.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc6_3954.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc8_3429.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc9_2367.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd10_2368.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd11_3873.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd12_3481.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd13_2356.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd1_3448.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd3_1742.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd8_2644.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Ipf1_3815.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx2_0900.3.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx3_0920.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx3_2226.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx4_2242.3.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx5_2385.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx6_2623.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Isl2_3430.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Isx_3445.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lbx2_3869.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx1_2240.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx2_0953.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx3_3431.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx4_1719.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx5_2279.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx6_2272.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx6_3432.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx8_2247.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx9_3492.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lmx1a_2238.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lmx1b_3433.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Meis1_2335.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Meox1_2310.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Mrg1_2246.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Mrg2_2302.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Msx1_3031.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Msx2_3449.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Msx3_3206.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx1-1_3856.3.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx1-2_3214.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-2_2823.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-3_3435.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-4_3074.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-5_3436.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-6_3437.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-9_3082.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx3-1_2923.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx6-1_2825.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx6-1_2825.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx6-3_3446.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox1_3970.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox2_3438.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox3_3439.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox5_2284.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox5_3963.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox6_3440.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Og2x_3719.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Otp_3496.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Otx1_2325.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Otx2_3441.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pax4_3989.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pax6_3838.3.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pax7_3783.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pbx1_3203.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Phox2a_3947.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Phox2b_3948.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pitx1_2312.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pitx2_2274.3.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pitx3_3497.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pknox1_2364.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pknox2_3077.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou1f1_3818.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou2f1_3081.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou2f2_3748.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou2f3_3986.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou3f1_3819.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou3f2_2824.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou3f3_3235.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou3f4_3773.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou4f3_2791.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou6f1_1731.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou6f1_3733.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Prop1_3949.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Prrx1_3442.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Prrx2_3072.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Rax_3443.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Rhox11_1765.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Rhox11_2205.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Rhox6_4251.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Shox2_2641.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six1_0935.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six2_2307.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six3_1732.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six4_2860.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six6_2267.4.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six6_2267.5.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tcf1_2666.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tcf2_0913.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tgif1_2342.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tgif2_3451.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Titf1_1722.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tlx2_3498.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Uncx4.1_2281.2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Vax1_3499.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Vax2_3500.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Vsx1_1728.1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Aft1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Aro80.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Asg1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Bas1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cbf1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cep3.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cha4.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cup9.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ecm22.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Fhl1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Fkh1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Fkh2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gal4.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gat1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gat3.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gat4.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gcn4.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gln3.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gsm1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gzf3.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Hal9.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Leu3.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Lys14.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Matalpha2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mbp1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mcm1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Met32.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mga1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mig1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mig2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mig3.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ndt80.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Nhp6a.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Nhp6b.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Nrg1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Oaf1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pbf1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pbf2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pdr1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Phd1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pho2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pho4.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Put3.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rap1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rdr1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rds1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rds2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rgt1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rph1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rpn4.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rsc3.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rsc30.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rtg3.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sfl1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sfp1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sip4.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Skn7.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Smp1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Spt15.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Srd1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Stb3.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Stp2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Stp4.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sum1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sut2.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tbf1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tbs1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tea1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tec1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tye7.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ume6.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Usv1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Xbp1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yap1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yap6.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ybr239c.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ydr520c.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yer130c.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ygr067c.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ykl222c.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yll054c.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yml081w.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ynr063w.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yox1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ypr013c.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ypr015c.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ypr196w.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yrm1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yrr1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Cbf1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Ceh-22.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Oct-1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Rap1.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Zif268.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/PNAS08/Cgd2_3490.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/PNAS08/PF14_0633.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/PNAS08/PFF0200c.pwm
%%DATADIR%%/position_weight_matrix/UniPROBE/all_uniprobe.csv
%%DATADIR%%/primer3/drosophila.w.transposons.txt
%%DATADIR%%/primer3/humrep_and_simple.txt
%%DATADIR%%/primer3/rodent_ref.txt
%%DATADIR%%/primer3/rodrep_and_simple.txt
%%DATADIR%%/query_samples/RepeatsWithORF.uql
%%DATADIR%%/query_samples/SimpleGene.uql
%%DATADIR%%/samples/ABIF/A01.abi
%%DATADIR%%/samples/ACE/BL060C3.ace
%%DATADIR%%/samples/ACE/K26.ace
+%%DATADIR%%/samples/APR/DNA.apr
+%%DATADIR%%/samples/APR/gyrA.apr
%%DATADIR%%/samples/Assembly/chrM.fa
%%DATADIR%%/samples/Assembly/chrM.sam
%%DATADIR%%/samples/Assembly/chrM.sorted.bam
%%DATADIR%%/samples/CLUSTALW/COI.aln
%%DATADIR%%/samples/CLUSTALW/HIV-1.aln
%%DATADIR%%/samples/CLUSTALW/ty3.aln.gz
%%DATADIR%%/samples/EMBL/AF177870.emb
%%DATADIR%%/samples/EMBL/AL000263.emb
%%DATADIR%%/samples/FASTA/human_T1.fa
%%DATADIR%%/samples/FASTQ/eas.fastq
%%DATADIR%%/samples/GFF/5prime_utr_intron_A20.gff
%%DATADIR%%/samples/GFF/5prime_utr_intron_A21.gff
%%DATADIR%%/samples/Genbank/CVU55762.gb
%%DATADIR%%/samples/Genbank/NC_014267.1.gb
%%DATADIR%%/samples/Genbank/PBR322.gb
%%DATADIR%%/samples/Genbank/murine.gb
%%DATADIR%%/samples/Genbank/sars.gb
%%DATADIR%%/samples/HMM/aligment15900.hmm
%%DATADIR%%/samples/MMDB/1CRN.prt
%%DATADIR%%/samples/MMDB/2JQS.prt
%%DATADIR%%/samples/MSF/HMA.msf
%%DATADIR%%/samples/MSF/lipid8.msf
%%DATADIR%%/samples/MSF/pla2_20.msf
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%%DATADIR%%/workflow_samples/NGS/raw_chip.uwl
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%%DATADIR%%/workflow_samples/NGS/raw_ngs/dnaseq/dna_single.uwl
%%DATADIR%%/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_filtration_paired.uwl
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%%DATADIR%%/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_single.uwl
%%DATADIR%%/workflow_samples/NGS/raw_rna.uwl
%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_main.uwl
%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_main_paired.uwl
%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr.uwl
%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr_paired.uwl
%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset.uwl
%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset_paired.uwl
-%%DATADIR%%/workflow_samples/NGS/tuxedo.uwl
%%DATADIR%%/workflow_samples/NGS/unmapped_reads.uwl
-%%DATADIR%%/workflow_samples/NGS/variation_annotation.uwl
%%DATADIR%%/workflow_samples/Sanger sequencing/trim-and-align.uwl
%%DATADIR%%/workflow_samples/Scenarios/filter_matched.uwl
%%DATADIR%%/workflow_samples/Scenarios/find_inverted_repeats.uwl
%%DATADIR%%/workflow_samples/Scenarios/find_sequences.uwl
%%DATADIR%%/workflow_samples/Scenarios/gene_by_gene_report.uwl
%%DATADIR%%/workflow_samples/Scenarios/group_primers_pairs.uwl
%%DATADIR%%/workflow_samples/Scenarios/intersect_annotations.uwl
+%%DATADIR%%/workflow_samples/Scenarios/length_filter.uwl
%%DATADIR%%/workflow_samples/Scenarios/merge_sequence_annotation.uwl
%%DATADIR%%/workflow_samples/Scenarios/pcr.uwl
%%DATADIR%%/workflow_samples/Scenarios/remote_blasting.uwl
%%DATADIR%%/workflow_samples/Scenarios/translate_seq_and_compl.uwl
%%DATADIR%%/workflow_samples/Transcriptomics/SearchTFBS.uwl
%%DATADIR%%/workflow_samples/users/CASAVA FASTQ filter.usa
%%DATADIR%%/workflow_samples/users/Dump sequence info.usa
%%DATADIR%%/workflow_samples/users/FASTQ Trimmer.usa
%%DATADIR%%/workflow_samples/users/Get the first half of sequence.usa
%%DATADIR%%/workflow_samples/users/Get the second half of sequence.usa
+%%DATADIR%%/workflow_samples/users/LengthMarker.usa
%%DATADIR%%/workflow_samples/users/LinkData Fetch.usa
%%DATADIR%%/workflow_samples/users/QualityFilter.usa
%%DATADIR%%/workflow_samples/users/Read one sequence.usa