diff --git a/README.md b/README.md index 74df877368099e8e9e29834a36ebf67752349f6a..b884b1e8042fe2f29634fd49aca0178b294e7846 100644 --- a/README.md +++ b/README.md @@ -78,7 +78,7 @@ For each input organism: 1) create the json input file for the script 2) create the docker-compose.yml for the organism (+ default.conf and edit main_proxy nginx default.conf for docker-compose docker configuration) 3) create the directory tree structure (if it already exists, only create the required directories) -4) gather files in the "source data" directory tree, can recursively search the directory (by default, the source-data folder is fixed for phaeoexplorer data, this default fixed directory can be set in the attributes of the Autoload class in autoload.py, can also be set as a command line argument with ```--source-data-folder <folder>```) +4) gather files in the "source data" directory tree, can recursively search the directory (by default, the source-data folder is fixed for phaeoexplorer data, this default fixed directory can be set in the attributes of the Autoload class in autoload.py. 5) link the source files to the organism correct src_data folders 6) modify headers in the transcripts and protein fasta files 7) generate blast banks (no commit) @@ -98,6 +98,18 @@ For integrated organisms you want to update with new data (the input shouldn't c ``` python3 autoload.py input.xlsx --update ``` +## Usage (development): + +autoload.py example: +``` +python3 autoload.py input.xlsx --init-instance --load-data --run-main +``` + +docker_compose_generator.py example: +``` +python3 docker_compose_generator.py --genus genus --species species --mode compose --dir . --template compose_template.yml +``` + ## Requirements: diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..35c00c4c948913d7daa1b3c9f4b3855afb86a6ae --- /dev/null +++ b/requirements.txt @@ -0,0 +1,20 @@ +bioblend==0.13.0 +boto==2.49.0 +certifi==2019.11.28 +cffi==1.14.0 +chardet==3.0.4 +cryptography==2.8 +idna==2.9 +numpy==1.18.1 +pandas==1.0.3 +pycparser==2.20 +pyOpenSSL==19.1.0 +PySocks==1.7.1 +python-dateutil==2.8.1 +pytz==2019.3 +PyYAML==5.3.1 +requests==2.23.0 +requests-toolbelt==0.9.1 +six==1.14.0 +urllib3==1.25.7 +xlrd==1.2.0