Installing add-ons with EP-manage.pl

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ExpressionPlot has several different categories of add-ons, all of which can be managed using the script util/EP-manage.pl:


EP-manage.pl

The EP-manage.pl is used to download and install these add-ons. It is located in the util/ subdirectory of the expressionplot hierarchy (run expressionplot-config if you don't know where this is on your installation). The same basic commands are used for the different categories of add-ons. The following examples show the commands for managing annotations, but they work the same for other types by changing annot to array, index, map, project or version. You can also run EP-manage.pl without arguments to get a more detailed usage message.

The following command will list the annotations available for download from the repository:

 EP-manage.pl list repos_annot

This command will list those already installed, additionally giving some information about each annotation:

 EP-manage.pl list local_annot -D

To install or update an annotation from the repository use a command like this, which would get an annotation for the mouse genome mm9:

 EP-manage.pl get_annot mm9

annot

annot refers to an annotation for a particular genome.

The annotations generally consist of genes (UCSC, Ensembl), alternative cassette exons, alternative retained introns, alternative terminal exons. It includes both flat files (.tsv) as well as SQL databases, and EP-manage.pl will automatically unpack the download and install everything in its correct location.

The identifiers for the annotations are the genome assembly names, like "rn4" (rat) or "mm9" (mouse).

array

array refers to the library files as well as probe alignments for a particular microarray.

EP-manage.pl will automatically load the probe alignments into a MySQL table, and put the library files where the array pipeline can find them.

The identifiers for the arrays are the short names for the arrays, like "MOE430" or "HuExon".

index

index refers to a set of bowtie index files (.ebwt).

EP-manage.pl will unpack and place them in the bowtie/indexes subdirectory.

For genomic indexes, the identifiers are the same as the genome, like "mm9" or "hg18". However, the junction indexes have longer names, like "rn4_ensembl_junctions.hjl=29", which also says the annotations upon which it was based and the "half-junction length", which you'll need to supply to ExpressionPlot using the -hjl swtich (in this case "-hjl 29"). Use list repos_index to list all the available indexes.

map

map refers to the files that map between annotations, or between different events of the same annotation.

EP-manage.pl will automatically place the maps in the annot/maps subdirectory and register them with ExpressionPlot so that they can be automatically found by the appropriate scripts.

The identifiers for the maps are the names of the two annotations joined by a dash, like "mm9-hg18", or the name of a single annotation, for a within-annotation map.

project

project refers to a data set, which could be just raw data or could be fully processed data, ready to be served by the front end. This offers a mechanism by which users can install example data sets, but also by which different ExpressionPlot servers can share data.

EP-manage.pl will automatically unpack the project to the projects/ subdirectory. It will then check if the project looks like it was fully processed. If it does, then it will register it with ExpressionPlot so you can start using it with the front end. To make it available right away, be sure to supply the "-a admin" switch to EP-manage.pl get_project so it can be assigned an administrator in the front end. For example, to install a project called "HumanTissues" with the administrator name "maliqa" you would use the following command:

 EP-manage.pl get_project HumanTissues -a maliqa

version

version refers to a version of ExpressionPlot. This is the way to upgrade, since it only updates the base system. It will keep all your settings in config.ini, all your user information and permissions, as well as all your add-ons and projects. Backups are made of existing files.

You can supply a version number, like "0.3", or the string "current" for the latest version, which is determined by asking the server.