fix travis

mjoppich · Jul 25, 2018 · 263b11d · 263b11d
1 parent 440b750
commit 263b11d
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Showing 15 changed files with 20 additions and 26 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -8,27 +8,21 @@ compiler: gcc
 before_install:
  - pwd
  - sudo apt-get -qq update
- - sudo apt-get install -y build-essential git libssl-dev liblua5.2-dev libgl1-mesa-dev wget libfontconfig1 libdbus-1-dev libglu1-mesa-dev g++-4.8 gcc-4.8
- - sudo apt-get purge cmake
- - mkdir -p ~/cmake/ && cd ~/cmake && wget https://cmake.org/files/v3.7/cmake-3.7.2.tar.gz
- - tar xf cmake-3.7.2.tar.gz
- - cd cmake-3.7.2
- - ./configure
- - sudo make install
+ - sudo apt-get install -y build-essential git libssl-dev liblua5.2-dev libgl1-mesa-dev wget libfontconfig1 libdbus-1-dev libglu1-mesa-dev g++-4.8 gcc-4.8 cmake
  - cd ~
  - pwd
- - wget http://download.qt.io/official_releases/qt/5.7/5.7.0/qt-opensource-linux-x64-5.7.0.run
- - chmod u+x qt-opensource-linux-x64-5.7.0.run
- - sudo ./qt-opensource-linux-x64-5.7.0.run --verbose -platform minimal --script /home/travis/build/mjoppich/bioGUI/silent_qt_install.qs
+ - wget http://download.qt.io/official_releases/qt/5.11/5.11.1/qt-opensource-linux-x64-5.11.1.run
+ - chmod u+x qt-opensource-linux-x64-5.11.1.run
+ - sudo ./qt-opensource-linux-x64-5.11.1.run --verbose -platform minimal --script /home/travis/build/mjoppich/bioGUI/silent_qt_install.qs
  - ls /usr/local/qt/
- - ls /usr/local/qt/5.7/
- - export PATH=/usr/local/qt/5.7/gcc_64/bin/:$PATH
+ - ls /usr/local/qt/5.11.1/
+ - export PATH=/usr/local/qt/5.11.1/gcc_64/bin/:$PATH
  - cd /home/travis/build/mjoppich/bioGUI
 
 
 before_script:
   - mkdir build
   - cd build
-  - PATH=/usr/local/qt/5.7/gcc_64/bin/:$PATH cmake ..
+  - PATH=/usr/local/qt/5.11.1/gcc_64/bin/:$PATH cmake ..
 
 script: make
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -114,7 +114,7 @@ if (UNIX AND NOT APPLE)
     message(STATUS ">>> Linux")
 
     set(Qt5_DIR "")
-    LIST(APPEND Qt5_DIR "~/Qt/5.8/gcc_64/" "~/Qt/5.7/gcc_64/" "/usr/local/qt/5.7/gcc_64/" "/home/mjoppich/qt/qt-everywhere-src-5.10.0/qtbase" "/opt/Qt5.10.0/5.10.0/gcc_64/")
+    LIST(APPEND Qt5_DIR "~/Qt/5.8/gcc_64/" "~/Qt/5.7/gcc_64/" "/usr/local/qt/5.11.1/gcc_64/" "/home/mjoppich/qt/qt-everywhere-src-5.10.0/qtbase" "/opt/Qt5.10.0/5.10.0/gcc_64/")
 
     set(ENV{OPENSSL_ROOT_DIR} "/home/users/joppich/libs/openssl/")
     set(ENV{LUA_DIR} "/home/users/joppich/libs/lua/")

diff --git a/extlib/openssl/openssl.exe b/extlib/openssl/openssl.exe
diff --git a/install_templates/install_ballgown.igui b/install_templates/install_ballgown.igui
@@ -122,7 +122,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-nc $IP $PORT << EOF
+nc -q 0 $IP $PORT <<EOF
 
 <template description="Ballgown: Isoform-level differential expression analysis in R." title="${PROGNICE}">
 <window title="${PROGNICE}">

diff --git a/install_templates/install_bowtie1.igui b/install_templates/install_bowtie1.igui
@@ -57,7 +57,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-nc $IP $PORT << EOF
+nc -q 0 $IP $PORT <<EOF
 
 <template description="bowtie 1.1.2 aligner" title="bowtie 1.1.2">
 <window title="bowtie 1.1.2 aligner">

diff --git a/install_templates/install_bowtie2.igui b/install_templates/install_bowtie2.igui
@@ -57,7 +57,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-nc $IP $PORT << EOF
+nc -q 0 $IP $PORT <<EOF
 
 <template description="bowtie2 2.0.4 aligner" title="bowtie2 2.0.4">
 <window title="bowtie2 2.0.4 aligner">

diff --git a/install_templates/install_glimmer.igui b/install_templates/install_glimmer.igui
@@ -65,7 +65,7 @@ echo "sending template"
 IP=$4
 PORT=$5
 
-nc $IP $PORT << EOF
+nc -q 0 $IP $PORT <<EOF
 <!--<?xml version="1.0" encoding="UTF-8")>-->
 <template description="Glimmer3 scripts ($PROG)" title="Glimmer3">
 

diff --git a/install_templates/install_hisat.igui b/install_templates/install_hisat.igui
@@ -61,7 +61,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-nc $IP $PORT << EOF
+nc -q 0 $IP $PORT <<EOF
 
 <template description="hisat2 2.0.5 aligner" title="hisat2 2.0.5">
 <window title="hisat2 2.0.5 aligner">

diff --git a/install_templates/install_hmmer.igui b/install_templates/install_hmmer.igui
@@ -52,7 +52,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-nc $IP $PORT << EOF
+nc -q 0 $IP $PORT <<EOF
 <template rootid="hmmerroot" description="HMMER ($PROG)" title="HMMER">
 
 <window width="500" height="800" title="HMMER">

diff --git a/install_templates/install_jellyfish.igui b/install_templates/install_jellyfish.igui
@@ -46,7 +46,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-nc $IP $PORT << EOF
+nc -q 0 $IP $PORT <<EOF
 <template rootid="blubb" intatt="111" description="Jellyfish ($PROG)" title="Jellyfish">
 
 <window width="500" height="1900" title="Jellyfish">

diff --git a/install_templates/install_rmats.igui b/install_templates/install_rmats.igui
@@ -53,7 +53,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-nc $IP $PORT << EOF
+nc -q 0 $IP $PORT <<EOF
 
 <template description="rMATS replicate MATS" title="$PROGNICE">
  <window title="$PROGNICE">

diff --git a/install_templates/install_rsem.igui b/install_templates/install_rsem.igui
@@ -59,7 +59,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-nc $IP $PORT << EOF
+nc -q 0 $IP $PORT <<EOF
 
 <template description="RSEM: estimating gene/isoform expression levels" title="$PROGNICE">
  <window title="$PROGNICE">

diff --git a/install_templates/install_stringtie.igui b/install_templates/install_stringtie.igui
@@ -59,7 +59,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-nc $IP $PORT << EOF
+nc -q 0 $IP $PORT <<EOF
 
 <template description="StringTie Transcript Assembler" title="${PROGNICE}">
 <window title="StringTie 1.3.0">

diff --git a/install_templates/install_trimmomatic.igui b/install_templates/install_trimmomatic.igui
@@ -53,7 +53,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-nc $IP $PORT << EOF
+nc -q 0 $IP $PORT <<EOF
 <template description="Trimming short RNA-Seq Reads" title="$PROGNICE">
  <window title="$PROGNICE">
   <vgroup>

diff --git a/install_templates/install_wsl_first.igui b/install_templates/install_wsl_first.igui
@@ -8,7 +8,7 @@ echo "Dependencies: build-essential dos2unix"
 if [ ! "$2" = "" ]; then
 	echo "Installing dependencies"
 	echo $2 | sudo -S apt-get update
-	echo $2 | sudo -S apt-get -y install build-essential dos2unix unzip
+	echo $2 | sudo -S apt-get -y install build-essential dos2unix unzip git cmake
 
 	echo "Enjoy bioGUI!"
 else