The latest information about Galaxy is available via https://galaxyproject.org/

Galaxy Quickstart

Galaxy requires Python 2.7 To check your python version, run:

$ python -V
Python 2.7.3

Start Galaxy:

$ sh run.sh

Once Galaxy completes startup, you should be able to view Galaxy in your browser at:

http://localhost:8080

Configuration & Tools

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.

Issues and Galaxy Development

Please see CONTRIBUTING.md .

Roadmap

Interested in the next steps for Galaxy? Take a look at the roadmap.

ImmPort Galaxy Set up

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-dev

Install 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 install

Add 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==1.12.9

Compile 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 -lm

Feel free to contact the ImmPort Galaxy team if you have any questions: [email protected]