From 54462b98a0d6fb3e66a1ea469618e8dccf60ebaa Mon Sep 17 00:00:00 2001 From: cb-Hades <81743695+cb-Hades@users.noreply.github.com> Date: Wed, 17 Jul 2024 11:20:26 +0200 Subject: [PATCH] small changes #7 --- README.md | 2 +- docs/source/cmpb/run-pipeline.rst | 5 ++++- pyproject.toml | 1 - src/specimen/data/config/cmpb_config.yaml | 3 ++- 4 files changed, 7 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 15083a5..200784d 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ SPECIMEN is a collection of different workflows designed for the automated and standardised curation of genome-scale models. It is mainly based on the [refineGEMs toolbox](https://github.com/draeger-lab/refinegems/tree/dev-2), but also includes additional tools like [CarveMe](https://carveme.readthedocs.io/en/latest/). -> Note: This tool is currently still under active developement, any feedback or ides are welcome. +> Note: This tool is currently still under active developement, any feedback or ideas are welcome. Currently avaible workflow: diff --git a/docs/source/cmpb/run-pipeline.rst b/docs/source/cmpb/run-pipeline.rst index 092de98..4adb75f 100644 --- a/docs/source/cmpb/run-pipeline.rst +++ b/docs/source/cmpb/run-pipeline.rst @@ -57,7 +57,10 @@ from inside a Python script or Jupyter Notebook with "config.yaml" being the pat The pipeline has two obligatory parameters: -- The path to the annotated genome file (if a model is given, should be the file used to create it) +- Path to a model + + - If no model is given, the `protein_fasta` needs to be provided. The format needs to be the same as the files provides by NCBI under `` -> `ftp` -> `_translated_cds.faa.gz` + - A media configuration (from refineGEMs) for testing the model's growth Further data can be added as available and/or needed (all are completely optional): diff --git a/pyproject.toml b/pyproject.toml index bfcd5e9..d8109ca 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -49,7 +49,6 @@ docs = ["accessible-pygments", "sphinx_copybutton", "pip-tools"] -# @TODO: [project.urls] repository = 'https://github.com/draeger-lab/SPECIMEN' documentation = 'https://specimen.readthedocs.io/en/latest/' diff --git a/src/specimen/data/config/cmpb_config.yaml b/src/specimen/data/config/cmpb_config.yaml index 576f354..834ee0c 100644 --- a/src/specimen/data/config/cmpb_config.yaml +++ b/src/specimen/data/config/cmpb_config.yaml @@ -15,7 +15,7 @@ input: modelpath: NULL # Optional, path to a model. # If not given, runs CarveMe -> Future update! - annotated_genome: __USER__ # Required, path to the annotated genome file + # annotated_genome: USER # Some alternative input if not model is given mediapath: __USER__ # Path to a media config to test growth with # General options @@ -46,6 +46,7 @@ cm-polish: email: USER # User Mail to use for Entrez protein_fasta: USER # Optional, except for 'is_lab_strain: True'. # The path to the protein FASTA used to create the CarveMe model. + # For more information, please refer to the documentation. is_lab_strain: False # Whether the users strain originates from a lab # Needs to be set to ensure that protein IDs get the 'bqbiol:isHomologTo' qualifier # & to set the locus_tag to the ones obtained by the annotation