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: ...@@ -53,13 +53,11 @@ repository can contain the following elements:
* scripts/ (directory with scripts for modules) * scripts/ (directory with scripts for modules)
PSOT uses a repository search path to find bundled and own repositories. It can 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 be set by defining the environment variable `PSOT_REPOSITORIES` with a ':'
':' separated list of paths or by passing the repositories via one or multiple separated list of paths.
`-r` arguments.
The repositories are loaded in the following order. Later respositories The repositories are loaded in the following order. Later respositories
overwrite values from previous repositories. overwrite values from previous repositories.
* default repository * default repository
* PSOT_REPOSITORIES * PSOT_REPOSITORIES
* `-r` repositories
...@@ -12,8 +12,10 @@ Welcome to PSOT - protein sequence observation tool's documentation! ...@@ -12,8 +12,10 @@ Welcome to PSOT - protein sequence observation tool's documentation!
concepts concepts
installation installation
usage.rst
modules modules
profiles profiles
repositories
Indices and tables Indices and tables
......
...@@ -31,11 +31,29 @@ Install nextflow:: ...@@ -31,11 +31,29 @@ Install nextflow::
curl -fsSL get.nextflow.io | bash 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:: Clone the git repository of PSOT::
git clone git@git.computational.bio.uni-giessen.de:SOaAS/psot.git 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 ...@@ -5,7 +5,7 @@ Modules
A module specifies exactly one analysis that can be run within PSOT. Each 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 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 phase. The phases are implemented as commandline tools that have at least the
following parameters: following parameters:
...@@ -19,6 +19,10 @@ following parameters: ...@@ -19,6 +19,10 @@ following parameters:
* ``--result`` - the result from the analysis step * ``--result`` - the result from the analysis step
* ``--output`` - the converted json file * ``--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:: A module manifest has the following structure::
# Module manifest for the blastp against swissprot analysis # Module manifest for the blastp against swissprot analysis
...@@ -45,5 +49,4 @@ A module manifest has the following structure:: ...@@ -45,5 +49,4 @@ A module manifest has the following structure::
parameters: parameters:
dbxref: UniProtKB/Swiss-Prot 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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