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iVar
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Note:
sort and index commands are very useful to setup a pipeline using iVar.iVar is available on bioconda. To install conda, please use the miniconda package. After intalling conda please add the following channels,
To install iVar,
iVar can be installed using Homebrew.
Xcode from Apple is required to compile iVar (and other tools) from source. If you don't want to install the full Xcode package from the AppStore, you can install the Xcode command line tools,
GNU Autotools is required to compile iVar from source.
To install Autotools using homebrew please use the command below,
HTSlib can be installed with conda using the command,
The conda binary is by default installed at /opt/. You can check the installation location by running the following command,
The output of the command will be in this format - /opt/conda/bin/conda or /opt/anaconda2/bin/conda or /opt/anaconda3/bin/conda depending on whether you installed miniconda or anaconda.
If the output is for example, /opt/conda/bin/conda, then you can add the path to the lib folder to $LD_LIBRARY_PATH using the command below. You can add this to your ~/.bash_profile or ~/.bashrc to avoid rerunning the command everytime a new bash session starts.
Installation instructions and downloads for HTSlib can be found at http://www.htslib.org/download/.
If HTSlib is installed in a non standard location, please add the following to your .bash_profile so that iVar can find HTSlib dynamic libraries during runtime.
To install iVar, run the following commands.
If HTSlib was installed using conda, please run the following commands by supplying the prefix to the bin folder of the conda binary.
The prefix to the bin folder can be found using the command which conda. The output of the command will be in this format - /opt/conda/bin/conda or /opt/anaconda2/bin/conda or /opt/anaconda3/bin/conda depending on whether you installed miniconda or anaconda. For example, if the output of the command is /opt/conda/bin/conda, the prefix to the htslib bin folder will be /opt/conda. This can be supplied to ./configure –with-hts=/opt/conda.
If HTSlib was installed in a non standard location, please run the following commands,
To test installation just run, ivar version and you should get the following output,
GNU Autotools is required to compile iVar from source.
To install Autotools using APT please use the command below,
HTSlib can be installed with conda using the command,
The conda binary is by default installed at /opt/. You can check the installation location by running the following command,
The output of the command will be in this format - /opt/conda/bin/conda or /opt/anaconda2/bin/conda or /opt/anaconda3/bin/conda depending on whether you installed miniconda or anaconda.
If the output is for example, /opt/conda/bin/conda, then you can add the path to the lib folder to $LD_LIBRARY_PATH using the command below. You can add this to your ~/.bash_profile or ~/.bashrc to avoid rerunning the command everytime a new bash session starts.
Installation instructions and downloads for HTSlib can be found at http://www.htslib.org/download/.
If HTSlib is installed in a non standard location, please add the following to your .bash_profile so that iVar can find HTSlib dynamic libraries during runtime.
To install iVar, run the following commands.
If HTSlib was installed using conda, please run the following commands by supplying the prefix to the bin folder of the conda binary.
The prefix to the bin folder can be found using the command which conda. The output of the command will be in this format - /opt/conda/bin/conda or /opt/anaconda2/bin/conda or /opt/anaconda3/bin/conda depending on whether you installed miniconda or anaconda. For example, if the output of the command is /opt/conda/bin/conda, the prefix to the htslib bin folder will be /opt/conda. This can be supplied to ./configure –with-hts=/opt/conda.
If HTSlib was installed in a non standard location, please run the following commands,
To test installation just run, ivar version and you should get the following output,
iVar can also be run via Docker. Pull the docker image from Docker Hub using the following command,
This docker image contains all the required dependencies to run iVar and the pipelines developed using iVar. You will have to attach a docker volume to get data into the docker container. Instructions to do so are in the Docker docs.
For bug reports please email gkarthik[at]scripps.edu or raise an issue on Github.
1.9.5