Commit 8176e9cd authored by Lukas Jelonek's avatar Lukas Jelonek
Browse files

Update documentation

parent 0c33a710
......@@ -53,13 +53,11 @@ repository can contain the following elements:
* scripts/ (directory with scripts for modules)
PSOT uses a repository search path to find bundled and own repositories. It can
be either set by defining the environment variable `PSOT_REPOSITORIES` with a
':' separated list of paths or by passing the repositories via one or multiple
`-r` arguments.
be set by defining the environment variable `PSOT_REPOSITORIES` with a ':'
separated list of paths.
The repositories are loaded in the following order. Later respositories
overwrite values from previous repositories.
* default repository
* PSOT_REPOSITORIES
* `-r` repositories
......@@ -12,8 +12,10 @@ Welcome to PSOT - protein sequence observation tool's documentation!
concepts
installation
usage.rst
modules
profiles
repositories
Indices and tables
......
......@@ -31,11 +31,29 @@ Install nextflow::
curl -fsSL get.nextflow.io | bash
(Optional) create a virtual env::
virtualenv --python=python3 venv
source venv/bin/activate
Install dbxref and psot::
pip3 install git+https://git.computational.bio.uni-giessen.de/SOaAS/dbxref.git
pip3 install git+https://git.computational.bio.uni-giessen.de/SOaAS/psot.git
Install a default repository for your profiles and modules::
TODO
Developer setup
---------------
Clone the git repository of PSOT::
git clone git@git.computational.bio.uni-giessen.de:SOaAS/psot.git
Configuration
-------------
Install it into a virtualenv::
Adapt the paths in the config.yaml to your needs.
virtualenv --python=python3 venv; source venv/bin/activate;
pip3 install git+https://git.computational.bio.uni-giessen.de/SOaAS/dbxref.git
pip3 install -e .
......@@ -5,7 +5,7 @@ Modules
A module specifies exactly one analysis that can be run within PSOT. Each
module has a default configuration that is specified in its manifest. During the
execution a module will run through two phases: the analysis and the conversion
execution, a module will run through two phases: the analysis and the conversion
phase. The phases are implemented as commandline tools that have at least the
following parameters:
......@@ -19,6 +19,10 @@ following parameters:
* ``--result`` - the result from the analysis step
* ``--output`` - the converted json file
The scripts can have additional parameters. They can be set in the paramaters
section of the module manifest. The parameters can be overridden in the
profile.
A module manifest has the following structure::
# Module manifest for the blastp against swissprot analysis
......@@ -45,5 +49,4 @@ A module manifest has the following structure::
parameters:
dbxref: UniProtKB/Swiss-Prot
These parameters can be overridden in the profile.
Structure of a repository
=========================
A repository contains one or multiple modules and profiles. It defines a
directory structure.
A repository has the following structure::
./repository/
config.yaml
profiles/
profile1.yaml
profile2.yaml
modules/
module1.yaml
module2.yaml
scripts/
run_tool1.yaml
run_tool2.yaml
convert_tool1.yaml
convert_tool2.yaml
You can include your own repository by setting the PSOT_REPOSITORIES
environment variable.
PSOT usage
==========
PSOT comes along as the commandline tool `psot`. It has two subcommands::
info -> show information about available modules and profiles
analyze -> runs a profile for a protein fasta file
Basic execution
---------------
::
psot analyze -f myfasta.faa -o results -p fast
Live mode execution
-------------------
During live mode execution PSOT will output results for already finished
modules as soon they become ready into a subfolder `live` within the results
folder.
::
psot analyze -f myfasta.faa -o results -p fast -l
Cluster mode
------------
PSOT can take leverage of your compute cluster. At the moment it only supports
SGE. To use the cluster set the `-C` option.
::
psot analyze -f myfasta.faa -o results -p fast -l -C
Debug mode execution
--------------------
PSOT has a few options for debugging. You can specify the execution directory
for the generated nextflow script via `-e <path>` and output the configuration
state via `-d`. If `-e` and `-d` are both specified then the execution
directory will not be removed.
::
psot analyze -f myfasta.faa -o results -p fast -l -C -e ~/my_exec_dir -d
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