文件列表:

LICENSE (11367, 2022-02-01)
cwls-docker (0, 2022-02-01)
cwls-docker\clustalo.cwl (6499, 2022-02-01)
cwls-docker\dbfetch.cwl (1608, 2022-02-01)
cwls-docker\emboss_backtranambig.cwl (4092, 2022-02-01)
cwls-docker\emboss_backtranseq.cwl (3997, 2022-02-01)
cwls-docker\emboss_cpgplot.cwl (5166, 2022-02-01)
cwls-docker\emboss_dotmatcher.cwl (4620, 2022-02-01)
cwls-docker\emboss_dotpath.cwl (4684, 2022-02-01)
cwls-docker\emboss_dottup.cwl (4439, 2022-02-01)
cwls-docker\emboss_isochore.cwl (4089, 2022-02-01)
cwls-docker\emboss_matcher.cwl (5043, 2022-02-01)
cwls-docker\emboss_needle.cwl (5528, 2022-02-01)
cwls-docker\emboss_newcpgreport.cwl (5181, 2022-02-01)
cwls-docker\emboss_pepinfo.cwl (4100, 2022-02-01)
cwls-docker\emboss_pepstats.cwl (4397, 2022-02-01)
cwls-docker\emboss_pepwindow.cwl (4260, 2022-02-01)
cwls-docker\emboss_polydot.cwl (4549, 2022-02-01)
cwls-docker\emboss_seqret.cwl (5451, 2022-02-01)
cwls-docker\emboss_sixpack.cwl (5009, 2022-02-01)
cwls-docker\emboss_stretcher.cwl (4843, 2022-02-01)
cwls-docker\emboss_transeq.cwl (5103, 2022-02-01)
cwls-docker\emboss_water.cwl (4868, 2022-02-01)
cwls-docker\fasta.cwl (11348, 2022-02-01)
cwls-docker\fastm.cwl (10040, 2022-02-01)
cwls-docker\genewise.cwl (8633, 2022-02-01)
cwls-docker\hmmer3_hmmscan.cwl (6958, 2022-02-01)
cwls-docker\hmmer3_phmmer.cwl (7365, 2022-02-01)
cwls-docker\infernal_cmscan.cwl (4016, 2022-02-01)
cwls-docker\iprscan5.cwl (5264, 2022-02-01)
cwls-docker\kalign.cwl (5027, 2022-02-01)
cwls-docker\lalign.cwl (5563, 2022-02-01)
cwls-docker\mafft.cwl (5702, 2022-02-01)
cwls-docker\mapmi.cwl (5793, 2022-02-01)
cwls-docker\muscle.cwl (4147, 2022-02-01)
cwls-docker\mview.cwl (7003, 2022-02-01)
cwls-docker\ncbiblast.cwl (9761, 2022-02-01)
cwls-docker\pfamscan.cwl (5053, 2022-02-01)
... ...

# Common Workflow Language implementation for EBI Web Services CWL implementation for consuming [EMBL-EBI Bioinformatics Web Services tools' clients](https://github.com/ebi-wp/webservice-clients). These CWL files are generated from the EBI Job Dispatcher Web Services (XML) description with [https://github.com/ebi-wp/webservice-cwl-generator](https://github.com/ebi-wp/webservice-cwl-generator) ## Contents - **cwls** : cwl files for the EBI Web Service clients (using Python clients from [webservice-clients](https://github.com/ebi-wp/webservice-clients)) - **cwls-docker** : cwl files for the EBI Web Service clients (using Python clients from [webservice-clients](https://github.com/ebi-wp/webservice-clients) Docker image) - **jsons** : example json files for defining input values for parameters - **sequence** : example sequence files for testing - **workflows** : a set of workflows to highlight the use of the clients - **ymls** : example yml files for defining input values for parameters ## Getting Started ### How to install cwltool You will need cwl-runner ([cwltool](https://github.com/common-workflow-language/cwltool)) to run CWL descriptions. Official instructions on how to install cwltool are provided in https://github.com/common-workflow-language/cwltool ### How to install Docker (optional) [Docker](https://www.docker.com/) installation instructions are provided in https://docs.docker.com/install/ ### Running CWL for EBI tools using local Python clients (does not require Docker) You can find CWL definitions in [cwls](cwls) accompanied with predefined parameters defined in [ymls](ymls). Running these CWL files **expects** [webservice-clients](https://github.com/ebi-wp/webservice-clients) directory to be found alongside the `webservice-cwl` directory. *Note:* Before running cwltool, you need to defined your own values for the `sequence` (or `asequence` plus `bsequence`) parameters, including a required email address. ``` cwltool ./cwls/tcoffee.cwl ./ymls/tcoffee.yml ``` ### Running CWL for EBI tools (requires Docker) You can find CWL definitions in [cwls-docker](cwls-docker) accompanied with predefined parameters defined in [ymls](ymls). Running these CWL files **does not** require [webservice-clients](https://github.com/ebi-wp/webservice-clients) to be found alongside the `webservice-cwl` directory, as the Docker image has got all the necessary clients pre-installed. *Note:* Before running cwltool, you need to defined your own values for the `sequence` (or `asequence` plus `bsequence`) parameters, including a required email address. ``` cwltool ./cwls-docker/tcoffee.cwl ./ymls/tcoffee.yml ``` ## Chaining the tools into workflows You can view examples of workflows chaining multiple tools together and example input ymls in the [workflows](workflows) folder. ## Documentation More documentation about [EMBL-EBI Bioinformatics Web Services](https://www.ebi.ac.uk/seqdb/confluence/display/WEBSERVICES/EMBL-EBI+Web+Services) ## Contact and Support If you have any problems, suggestions or comments for our services please contact us via [EBI Support](http://www.ebi.ac.uk/support/index.php?query=WebServices). ## License The European Bioinformatics Institute - [EMBL-EBI](https://www.ebi.ac.uk/), is an Intergovernmental Organization which, as part of the European Molecular Biology Laboratory family, focuses on research and services in bioinformatics. Apache License 2.0. See [license](LICENSE) for details.

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