Merge pull request BackofenLab#53 from BackofenLab/intarna-2

Intarna 2.0.0 all commits

.gitignore

@@ -26,3 +26,42 @@
 *.exe
 *.out
 *.app
+
+# eclipse files
+.project
+.settings
+.cproject
+.autotools
+.*
+
+# temporary autotools files
+config.*
+Makefile
+autom4te.cache
+configure
+missing
+install-sh
+depcomp
+aclocal.m4
+Makefile.in
+compile
+*/.deps
+*/.deps/*
+/intaRNA-*.tar.gz
+
+
+# temp dir
+tmp
+tmp/*
+tests/logs
+tests/logs/*
+
+/1
+/RNAup
+/IntaRNA-1
+/IntaRNA-1.out2
+/q.fasta
+/q2.fasta
+/seq.fasta
+/t.fasta
+/t2.fasta

.travis.yml

@@ -1,15 +1,44 @@
-sudo: false
 language: cpp
 
+cache:
+  apt: true
+
+addons:
+  apt:
+    sources:
+    - ubuntu-toolchain-r-test
+    packages:
+    - gcc-4.9
+    - g++-4.9
+
 os:
-  - linux
+    - linux
+
 compiler:
-  - gcc
-
+    - gcc
+
+before_install:
+    - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
+    - chmod +x miniconda.sh
+    - "./miniconda.sh -b"
+    - export PATH=/home/travis/miniconda2/bin:$PATH
+    - conda update --yes conda
+    - conda install --yes viennarna automake boost -c conda-forge -c bioconda
+    - export CONDA_PATH=/home/travis/miniconda2/
+    - export CONDA_LIB_PATH=/home/travis/miniconda2/lib
+    - ls $CONDA_LIB_PATH
+    - ls $CONDA_PATH/include
+    - export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CONDA_LIB_PATH
+
 script:
- # download and compile ViennaRNA dependency
- - wget https://depot.galaxyproject.org/software/vienna_rna/vienna_rna_1.8_src_all.tar.gz
- - tar xvfz vienna_rna_1.8_src_all.tar.gz
- - cd ViennaRNA-1.8.5 && ./configure --prefix=$HOME/vienna --without-perl && make && make install
- - cd $TRAVIS_BUILD_DIR && ./configure --with-RNA=$HOME/vienna --prefix=$HOME/IntaRNA && make && make install
- - $HOME/IntaRNA/bin/IntaRNA -h
+    - RNAalifold --version
+    ##### start IntaRNA build #####
+    - cd $TRAVIS_BUILD_DIR 
+    # generate autotools's files 
+    - bash autotools-init.sh 
+    - CC=gcc-4.9 CXX=g++-4.9 ./configure --with-boost=$CONDA_PATH --with-RNA=$CONDA_PATH --prefix=$HOME/IntaRNA
+    # compile, test and install IntaRNA
+    - make && make tests && make install
+    ##### check IntaRNA build #####
+    # run IntaRNA with help output
+    - $HOME/IntaRNA/bin/IntaRNA -h

AUTHORS

@@ -1,3 +1,15 @@
-Anke Busch         http://www.bioinf.uni-freiburg.de/~abusch/
-Andreas Richter    http://www.bioinf.uni-freiburg.de/
-Sven Siebert
+
+#############################################################
+ version 2.*
+#############################################################
+
+- Martin Mann
+
+#############################################################
+ version 1.*
+#############################################################
+
+- Anke Busch
+- Andreas Richter 
+- Sven Siebert
+

COPYING

@@ -0,0 +1 @@
+see LICENSE file