Overview

• fast and flexible installation for full access to MiModD as a command line package
• easy to integrate with a local Galaxy installation at any time
• few installation requirements, in particular, on OS X

Detailed Instructions

Open a terminal window and try executing (possibly with superuser rights, i.e., with sudo prepended):

python3 -m pip install MiModD

By default, this will install MiModD from source on Linux systems and from a precompiled archive on compatible versions of OS X. For more complete instructions that include installation of required software see our installation examples.

Depending on your environment and needs you may wish to append some of the following options to the above command (for a full list of pip installation options type python3 -m pip help install or read the online documentation):

--user

to install MiModD relative to the current user's home directory

This option is ideal for single-user installs and does not require write permission in system-wide installation directories.

--no-use-wheel

to force installation from source even if a precompiled archive is available for your system

This option is relevant only for OS X, for which we provide precompiled installation files, and in the hopefully rare event that the precompiled archive that pip chooses to install on your system turns out to be incompatible with your platform architecture.

Note that a source installation has an extended list of requirements (see above) compared to a wheel installation.

The installation may take a few minutes, but after it is finished, you can proceed to configure MiModD for your system.

The config tool

General usage:

python3 -m MiModD.config [--parameter VALUE] ...

python3 -m MiModD.config

% python3 -m MiModD.config

Which folder should MiModD use to store temporary data? [/var/tmp]:
In which folder should MiModD look for SnpEff? [/not configured]:
Up to how many threads do you want to allow MiModD to use at a time? [4]:3
Up to how much memory in GB do you want to allow MiModD to use? [2]:6

All necessary information has been collected.
Hit <Enter> to store your settings and start using MiModD.

To change settings later, you can rerun this tool with new settings
provided as command line options.


Settings for package MiModD in: /home/example/lib/python3.4/site-packages/MiModD

-----------------------
    PARAMETER : VALUE
    .......................
    TMPFILES_PATH : /var/tmp
    MAX_MEMORY : 6
    SNPEFF_PATH : /not configured
    MULTITHREADING_LEVEL : 3

python3 -m MiModD.config [--tmpfiles PATH] [--snpeff PATH] [-t THREADS] [-m MEMORY]

python3 -m MiModD.config --tmpfiles /var/tmp/mimodd_tmp -m 8

Configuration through an environment variable

As an alternative to command line configuration, you can provide new settings for the configuration parameters also through the MiModD-specific environment variable $MIMODD_CONFIG_UPDATE.

The value of this variable has to be set to a :-separated list of parameter=value entries, for example:

export MIMODD_CONFIG_UPDATE=MAX_MEMORY=8:MULTITHREADING_LEVEL=4

The presence of the environment variable will be detected by MiModD at its next run from the same terminal, and will be used to update the package settings accordingly.

You can also pass the variable exclusively to Galaxy by prepending it to the start script and this is the recommended approach to configure a Galaxy Tool Shed installation of MiModD:

MIMODD_CONFIG_UPDATE=MULTITHREADING_LEVEL=3:TMPFILES_PATH=home/galaxy/tmp/ sh run.sh

With this, the MiModD settings will get updated when the first MiModD tool gets executed from within the Galaxy instance.

Configuration parameters

listed as pairs of

PARAMETER : config options

where PARAMETER can be used in the $MIMODD_CONFIG_UPDATE variable and the config options are used to set the same parameter using the python3 -m MiModD.config command.

TMPFILES_PATH : --tmpfiles, --tmpfiles-path

the directory in which MiModD will store temporary files [default: /var/tmp]

In a typical analysis pipeline, MiModD may produce several GB of data in this directory and remove them automatically again when the data is not any longer needed. Under exceptional circumstances, however, MiModD might fail to delete data files, so this directory is the first place you should look at if you notice reduced disk space. Also, any users of MiModD will require write permission in this directory.

MULTITHREADING_LEVEL : -t, --threads

the maximum number of cores that a single MiModD command is supposed to use at any time [default: 4]

Many MiModD commands take advantage of multiprocessing to speed up analyses. These commands try to respect this setting if possible although some may use slightly more than their allocated CPU share.

MAX_MEMORY : -m, --memory

the maximum memory in GB that any single MiModD command should use [default: 2]

WGS data files are often very large and some MiModD tools can operate on them more efficiently when allowed to hold a larger portion of such files in memory at once. Most of the time MiModD will consume less than 1 GB though. The setting is adhered to relatively strictly by most tools with the exception of the SNAP aligner-based tools mimodd snap index, mimodd snap, mimodd snap_batch and the Galaxy SNAP Read Alignment tool. Due to the nature of their underlying alignment algorithm these tools will require a fixed amount of memory that depends on the size of the reference genome and which may be significantly more than the configured setting.

SNPEFF_PATH : --snpeff, --snpeff-path

the path to the optional SnpEff variant annotation tool

This parameter should be set to the directory that you installed SnpEff into (e.g., ~/snpEff if you followed the recommended installation steps). If you do not have SnpEff installed, keep the default setting, to have all SnpEff-dependent functionality of MiModD deactivated.