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use conda integrated package management within snakemake
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,16 +1,16 @@ | ||
| #!/bin/bash | ||
| set -euxo pipefail | ||
| HIPPUNFOLD_CACHE_DIR=`pwd`/test_data/fake_models | ||
| hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w | ||
| hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi R | ||
| hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi L | ||
| hippunfold test_data/bids_multiT2w test_out participant -np --modality T2w | ||
| hippunfold test_data/bids_T1w test_out participant -np --modality T1w | ||
| hippunfold test_data/bids_hippb500 test_out participant -np --modality hippb500 | ||
| hippunfold test_data/bids_T1w_longitudinal test_out participant -np --modality T1w | ||
| hippunfold test_data/bids_singleT2w_longitudinal test_out participant -np --modality T2w | ||
| hippunfold test_data/bids_manualseg test_out participant -np --modality manualseg --path_manualseg test_data/bids_manualseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz | ||
| hippunfold test_data/bids_manualseg_1hemi test_out participant -np --modality manualseg --hemi L | ||
| hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template | ||
| hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --output_space T1w | ||
| hippunfold test_data/bids_T1w test_out participant -np --modality T1w --use-template-seg | ||
| hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --use-conda | ||
| # hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi R | ||
| # hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi L | ||
| # hippunfold test_data/bids_multiT2w test_out participant -np --modality T2w | ||
| # hippunfold test_data/bids_T1w test_out participant -np --modality T1w | ||
| # hippunfold test_data/bids_hippb500 test_out participant -np --modality hippb500 | ||
| # hippunfold test_data/bids_T1w_longitudinal test_out participant -np --modality T1w | ||
| # hippunfold test_data/bids_singleT2w_longitudinal test_out participant -np --modality T2w | ||
| # hippunfold test_data/bids_manualseg test_out participant -np --modality manualseg --path_manualseg test_data/bids_manualseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz | ||
| # hippunfold test_data/bids_manualseg_1hemi test_out participant -np --modality manualseg --hemi L | ||
| # hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template | ||
| # hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --output_space T1w | ||
| # hippunfold test_data/bids_T1w test_out participant -np --modality T1w --use-template-seg |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,8 @@ | ||
| name: env1 | ||
| channels: | ||
| - conda-forge | ||
| - defaults | ||
| dependencies: | ||
| - python=3.9 | ||
| - nibabel=5.2.1 | ||
| - numpy=2.1.2 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| name: env2 | ||
| channels: | ||
| - conda-forge | ||
| - defaults | ||
| dependencies: | ||
| - python=3.9 | ||
| - connectome-workbench=2.0.1 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,9 @@ | ||
| name: env3 | ||
| channels: | ||
| - conda-forge | ||
| - defaults | ||
| dependencies: | ||
| - python=3.9 | ||
| - nibabel=5.2.1 | ||
| - numpy=2.1.2 | ||
| - scipy=1.13.1 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| name: env4 | ||
| channels: | ||
| - conda-forge | ||
| - defaults | ||
| dependencies: | ||
| - python=3.9 | ||
| - ants |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,131 @@ | ||
| channels: | ||
| - conda-forge | ||
| - defaults | ||
| dependencies: | ||
| - python=3.9 | ||
| - annotated-types=0.7.0 | ||
| - appdirs=1.4.4 | ||
| - argparse-dataclass=2.0.0 | ||
| - arrow=1.3.0 | ||
| - astor=0.8.1 | ||
| - astroid=2.15.8 | ||
| - atomicwrites=1.4.1 | ||
| - attrs=23.2.0 | ||
| - bids-validator=1.14.6 | ||
| - black=22.12.0 | ||
| - boutiques=0.5.26 | ||
| - certifi=2024.7.4 | ||
| - charset-normalizer=3.3.2 | ||
| - click=8.1.7 | ||
| - colorama=0.4.6 | ||
| - conda-inject=1.3.2 | ||
| - configargparse=1.7 | ||
| - connection-pool=0.0.3 | ||
| - copier=9.3.1 | ||
| - datrie=0.8.2 | ||
| - dill=0.3.8 | ||
| - docopt=0.6.2 | ||
| - docutils=0.20.1 | ||
| - dpath=2.2.0 | ||
| - dunamai=1.22.0 | ||
| - eval-type-backport=0.2.0 | ||
| - fastjsonschema=2.20.0 | ||
| - flake8=4.0.1 | ||
| - formulaic=0.5.2 | ||
| - funcy=2.0 | ||
| - gitdb=4.0.11 | ||
| - gitpython=3.1.43 | ||
| - graphlib-backport=1.1.0 | ||
| - greenlet=3.0.3 | ||
| - humanfriendly=10.0 | ||
| - idna=3.7 | ||
| - immutables=0.21 | ||
| - importlib-metadata=8.1.0 | ||
| - importlib-resources=6.4.0 | ||
| - iniconfig=2.0.0 | ||
| - interface-meta=1.3.0 | ||
| - isort=5.13.2 | ||
| - jinja2=3.1.4 | ||
| - jinja2-ansible-filters=1.3.2 | ||
| - jinja2-time=0.2.0 | ||
| - jsonschema=4.23.0 | ||
| - jsonschema-specifications=2023.12.1 | ||
| - jupyter-core=5.7.2 | ||
| - lazy-loader=0.4 | ||
| - lazy-object-proxy=1.10.0 | ||
| - markupsafe=2.1.5 | ||
| - mccabe=0.6.1 | ||
| - more-itertools=9.1.0 | ||
| - mypy-extensions=1.0.0 | ||
| - nbformat=5.10.4 | ||
| - nibabel=5.2.1 | ||
| - num2words=0.5.13 | ||
| - numpy=2.1.2 | ||
| - packaging=23.2 | ||
| - pandas=2.2.3 | ||
| - pastel=0.2.1 | ||
| - pathspec=0.12.1 | ||
| - pkgutil-resolve-name=1.3.10 | ||
| - plac=1.4.3 | ||
| - platformdirs=4.2.2 | ||
| - pluggy=1.5.0 | ||
| - plumbum=1.9.0 | ||
| - poethepoet=0.10.0 | ||
| - prompt-toolkit=3.0.36 | ||
| - psutil=6.0.0 | ||
| - pulp=2.7.0 | ||
| - pvandyken-deprecated=0.0.4 | ||
| - py=1.11.0 | ||
| - pybids=0.16.5 | ||
| - pycodestyle=2.8.0 | ||
| - pydantic=2.9.2 | ||
| - pydantic-core=2.23.4 | ||
| - pyflakes=2.4.0 | ||
| - pygments=2.18.0 | ||
| - pygraphviz=1.7 | ||
| - pylint=2.17.7 | ||
| - pyreadline3=3.4.1 | ||
| - pytest=6.2.5 | ||
| - pytest-console-scripts=1.4.1 | ||
| - python-dateutil=2.9.0.post0 | ||
| - pytz=2024.1 | ||
| - pywin32=306 | ||
| - pyyaml=6.0.1 | ||
| - questionary=2.0.1 | ||
| - referencing=0.35.1 | ||
| - requests=2.32.3 | ||
| - reretry=0.11.8 | ||
| - rpds-py=0.19.0 | ||
| - ruamel-yaml=0.18.6 | ||
| - ruamel-yaml-clib=0.2.8 | ||
| - scipy=1.13.1 | ||
| - simplejson=3.19.2 | ||
| - six=1.16.0 | ||
| - smart-open=7.0.4 | ||
| - smmap=5.0.1 | ||
| - snakebids=0.13.1 | ||
| - snakefmt=0.8.0 | ||
| - snakemake=8.23.0 | ||
| - snakemake-interface-common=1.17.4 | ||
| - snakemake-interface-executor-plugins=9.3.2 | ||
| - snakemake-interface-report-plugins=1.1.0 | ||
| - snakemake-interface-storage-plugins=3.3.0 | ||
| - sqlalchemy=2.0.31 | ||
| - stopit=1.1.2 | ||
| - tabulate=0.9.0 | ||
| - termcolor=2.4.0 | ||
| - throttler=1.2.2 | ||
| - toml=0.10.2 | ||
| - tomli=2.0.1 | ||
| - tomlkit=0.13.0 | ||
| - toposort=1.10 | ||
| - traitlets=5.14.3 | ||
| - types-python-dateutil=2.9.0.20240316 | ||
| - typing-extensions=4.12.2 | ||
| - tzdata=2024.1 | ||
| - urllib3=2.2.2 | ||
| - wcwidth=0.2.13 | ||
| - wrapt=1.16.0 | ||
| - yte=1.5.4 | ||
| - zipp=3.19.2 | ||
| name: env1 |
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