The latest information about Galaxy is available via https://galaxyproject.org/
Galaxy requires Python 2.7 To check your python version, run:
$ python -V
Python 2.7.3Start Galaxy:
$ sh run.shOnce Galaxy completes startup, you should be able to view Galaxy in your browser at:
You may wish to make changes from the default configuration. This can be done in the config/galaxy.ini file.
- Tools can be either installed from the Tool Shed or added manually.
For details please see the tutorial.
Note that not all dependencies for the tools provided in the tool_conf.xml.sample are included. To install them please visit "Manage dependencies" in the admin interface.
Please see CONTRIBUTING.md .
Interested in the next steps for Galaxy? Take a look at the roadmap.
To run the tools for ImmPort Galaxy smoothly, the following dependencies are required:
$ apt-get install gfortran g++
$ apt-get install libreadline-dev libX11-dev xorg-dev python-dev
$ apt-get install libcurl4-openssl-dev libxml2-dev libbz2-dev
$ apt-get install liblzma-dev libpcre3-dev
$ apt-get install libhdf5-serial-dev libhdf5-dev mesa-common-dev libglu1-mesa-devInstall R:
$ curl -O https://cran.r-project.org/src/base/R-3/R-3.3.0.tar.gz
$ gzip -cd R-3.3.0.tar.gz | tar xvf -
$ cd R-3.3.0
$ ./configure --prefix=/home/galaxy/opt/R-3.3.0-Shared --with-tcltk --enable-R-shlib
$ make
$ make installAdd R to your PATH. Within R, install the following packages:
>source("http://bioconductor.org/biocLite.R")
>biocLite()
>biocLite("flowCore")
>biocLite("flowDensity")
>biocLite("flowCL")
>biocLite("flowAI")
>install.packages("plyr",repos="http://cran.r-project.org")
>install.packages("ggplot2",repos="http://cran.r-project.org")
>biocLite("flowViz")
>biocLite("ncdfFlow")
>biocLite("rgl")
>biocLite("ks")
>biocLite("flowWorkspace")
>biocLite("flowStats")
>biocLite("flowVS")
>biocLite("ggcyto")Install required python packages in the galaxy virtual environment:
$ cd /home/galaxy/immport-galaxy
$ . .venv/bin/activate
$ pip install numpy==1.9.2
$ pip install matplotlib
$ pip install pandas==0/18.0
$ pip install jinja2
$ pip install rpy2
$ pip install scipy==0.17.0
$ pip install plotly==1.12.9Compile FLOCK. The binaries are included in $GALAXY_HOME/tools/flowtools/src.
$ cd $GALAXY_HOME/tools/flowtools/bin
$ cc -o flock1 ../src/flock1.c ../src/find_connected.c -lm
$ cc -o flock2 ../src/flock2.c -lm
$ cc -o cent_adjust ../src/cent_adjust.c -lmFeel free to contact the ImmPort Galaxy team if you have any questions: immport-galaxy@immport.org