diff --git a/exemplary_workflow/maestrowf/.gitignore b/exemplary_workflow/maestrowf/.gitignore deleted file mode 100644 index 53752db..0000000 --- a/exemplary_workflow/maestrowf/.gitignore +++ /dev/null @@ -1 +0,0 @@ -output diff --git a/exemplary_workflow/maestrowf/README.md b/exemplary_workflow/maestrowf/README.md deleted file mode 100644 index d009c4f..0000000 --- a/exemplary_workflow/maestrowf/README.md +++ /dev/null @@ -1,17 +0,0 @@ -# Maestrowf -Implementation of the exemplary workflow with [maestrowf](https://github.com/LLNL/maestrowf). - -## Installation -`maestrowf` itself can be installed via pip. It does not deploy the software stack for you, so -installing all required software first is required. You can do so by running the following commands. -```sh -conda env create --file ../source/envs/default_env.yml --prefix ./exemplarywf -conda activate exemplarywf -pip install maestrowf -``` - -## Running the simple use case -```sh -maestro run exemplarywf.yaml -o ./output -``` -It is recommended to specify the workspace with the `-o` option. diff --git a/exemplary_workflow/maestrowf/exemplarywf.yaml b/exemplary_workflow/maestrowf/exemplarywf.yaml deleted file mode 100644 index f37407d..0000000 --- a/exemplary_workflow/maestrowf/exemplarywf.yaml +++ /dev/null @@ -1,69 +0,0 @@ -description: - name: exemplary_workflow - description: A simple workflow which solves the poisson equation and shows the result in a PDF - - -env: - variables: - INPUT_PATH: ./../../../source - OUTPUT_PATH: ./output - # Note on dependencies taken from https://github.com/LLNL/maestrowf/blob/develop/samples/documentation/lulesh_sample1_unix_commented.yaml - #------------------------------- - # Dependencies - #------------------------------- - # Dependencies represent external artifacts that should be present before a - # workflow can run. These are things like acquirable inputs from a directory - # or a repository such as input files for programs, code, data, etc.. - - # NOTE: Currently there are only two types of dependencies: - # path - verifies the existence of the specified path before execution. - # git - clones the specified repository before execution of the study. - #------------------------------- - # dependencies: - # git: - # - name: WORKFLOWS - # path: $(OUTPUT_PATH) - # url: https://github.com/BAMResearch/NFDI4IngScientificWorkflowRequirements.git - - -study: - - name: generate-mesh - description: Generate a partition of the unit square. - run: - cmd: | - gmsh -2 -order 1 -format msh2 $(INPUT_PATH)/unit_square.geo -o $(OUTPUT_PATH)/unit_square.msh - depends: [] - - - name: convert-mesh - description: Convert the mesh to XDMF format. - run: - cmd: | - meshio convert $(OUTPUT_PATH)/unit_square.msh $(OUTPUT_PATH)/unit_square.xdmf - depends: [generate-mesh] - - - name: solve-poisson - description: Solve the poisson equation. - run: - cmd: | - python $(INPUT_PATH)/poisson.py --mesh $(OUTPUT_PATH)/unit_square.xdmf --degree 2 --outputfile $(OUTPUT_PATH)/poisson.pvd - depends: [convert-mesh] - - - name: paraview-rendering - description: Plot the solution with ParaView. - run: - cmd: | - pvbatch $(INPUT_PATH)/postprocessing.py $(OUTPUT_PATH)/poisson.pvd $(OUTPUT_PATH)/contourplot.png - depends: [solve-poisson] - - - name: copy - description: Copy the latex source code. - run: - cmd: | - cp $(INPUT_PATH)/paper.tex $(OUTPUT_PATH)/paper.tex - - - name: compile - description: Generate the PDF from latex code. - run: - cmd: | - tectonic $(OUTPUT_PATH)/paper.tex - depends: [copy, paraview-rendering] diff --git a/exemplary_workflow/planemo/README.md b/exemplary_workflow/planemo/README.md deleted file mode 100644 index f012f84..0000000 --- a/exemplary_workflow/planemo/README.md +++ /dev/null @@ -1,121 +0,0 @@ -# Planemo - -## Installation - -`planemo` can be installed via `pip` or `conda` (experimental). -See the [docs](https://planemo.readthedocs.io/en/latest/installation.html) -for more information. - - -## Log - -### Attempt 1 via conda -The following commands were executed. -If not stated explicitly everything worked as intended. - -Creation of the conda env: -```sh -mamba create -n planemo -c bioconda planemo -``` -Init demo project: -```sh -planemo project_init --template=demo mytools -cd mytools -``` - -```sh -planemo lint -planemo lint randomlines.xml -``` -This gives an AttributeError. - -```sh -planemo test randomlines.xml -``` -raises ImportError. - -Installation via `conda` seems to be broken. - -### Attempt 2 via pip - -1. deactivate conda. -2. follow install guide for pip. - -```sh -planemo l randomlines.xml -``` -seems to be okay. - -```sh -planemo test randomlines.xml -``` -git clone bare repos into `/home/pdiercks/.planemo/gx_repo` -downloads a whole lot of packages ... -... it installs miniconda3 ... wtf -... there is a lot of useless output. -... in the end 1 of 2 tests fails. nice demo. - -```sh -planemo l ./run_dolfin.cwl -``` -does not work because Node.js engine is required to -evaluate and validate JavaScript Expressions - -+ Loading cwltool is also experimental. -+ Linting of xml fails without hint why this might be the case. - -### What worked for me - -1. `git clone git@github.com:galaxyproject/galaxy.git ./galaxyroot` -2. `export GR=/home/pdiercks/repos/galaxyroot` -3. `cd /home/pdiercks/projects/planemo_demo/seqtk_example` -4. `planemo test --galaxy_root $GR` -5. `planemo serve --galaxy_root $GR` - -Any command like `planemo test | serve | run` will spin -up the galaxy instance. This takes quite some time even -if `--galaxy_root` is specified. -Basically all packages are uninstalled and installed again each time. - -#### Problem with planemo run - -FileNotFoundError: [Errno 2] No such file or directory: '/home/pdiercks/repos/galaxyroot/.venv/bin/galaxyctl' - -after I tried running one of the test workflows via: -```sh - ❯ planemo run --galaxy_root $GR tutorial.ga tutorial-job.yml --download_outputs --output_directory . --output_json output.json -``` - -### How to add tools - -[add-tool-tutorial](https://galaxyproject.org/admin/tools/add-tool-tutorial/) - -in this example the tool is a perl script `toolExample.pl`. -the corresponding wrapper is `toolExample.xml`. -Both are placed under `galaxyroot/tools/myTools` (need to `mkdir galaxyroot/tools/myTools`) -Add new lines to `galaxyroot/config/tool_conf.xml` to make galaxy aware of the new tool. - -### Galaxy Root - -```sh -cd $galaxy_root && sh run.sh -``` -can also be used to setup a Galaxy instance ... -it found my installation of mambaforge and installed -a virtualenv using that. (`~/mambaforge/envs/_galaxy_`) - -However, there were several errors and it fails. -This does not work. -Probably because one has to set the path for non-conda -python somehow and the virtualenv is faulty. - -I guess `planemo serve --galaxy_root` shoud be equivalent -to `sh run.sh` only that here I have the virtualenv setup correctly. - - -### Purge - -Delete the following to remove galaxy later on: -1. `~/repos/galaxyroot` -2. `~/.planemo` -3. `~/mambaforge/envs/_galaxy_`