Adding minimal Dockerfile for SCT. #1600
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perone
added
the
enhancement
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Yeah, could be useful, eg. for #1599. You're stating "minimal" but have you tried Ubuntu Core 2016? |
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I also think it could be useful for the #1599. I haven't tried Ubuntu Core 2016 but I guess it wouldn't work due to the number of dependencies in SCT, however, I don't have too much time to give it a try right now. |
peristeri
reviewed
Feb 14, 2018
| RUN apt-get update && apt-get install -y wget unzip git bzip2 | ||
| RUN wget https:/neuropoly/spinalcordtoolbox/archive/master.zip | ||
| RUN unzip master.zip | ||
| WORKDIR spinalcordtoolbox-master |
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A comment on how run commands. Each time RUN is called, a new volume is created. What I suggest is to move WORKDIR above the RUN command. And merge all the run commands into 1 RUN command.
RUN apt-get update && \
apt-get install -y wget unzip git bzip2 && \
wget https:/neuropoly/spinalcordtoolbox/archive/master.zip && \
unzip master.zip && \
...
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You mean layer ? Docker isn't going to create volumes every time RUN is called. When the RUN is executed, another layer is created on the top of the previous one. Since Docker uses Copy on Write (CoW), in this case, the final image size will be the same, so in my opinion, there will be no gains in merging all RUN commands together except for making it harder to read. I can merge them if you want, but I don't think it will be better though.
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Correction, you are right, it creates a new layer with each run. It is a question of best practice. But, it seams that it sounds like it is a duplicate of https:/neuropoly/docker , am I wrong?
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I wasn't able to find an Ubuntu Dockerfile at https:/neuropoly/docker, only a Debian image based on the Neurodebian. Let me know if you guys want me to close this PR without merging.
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no, i like the idea of having a container inside SCT repos, so i would keep this PR.
we need, however to associate a documentation with it, so that people know it exists and what to do with it.
this repos: https:/neuropoly/docker is made for the lab in general, not specific to SCT, so it might become messy at some point, without commit regulations, etc.
jcohenadad
approved these changes
Feb 16, 2018
jcohenadad
added a commit
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Feb 16, 2018
* jca-release: (88 commits) updated CHANGES.md Adding minimal Dockerfile for SCT. (#1600) Added a study in SCT applications section Fix TensorFlow installation on Debian (#1601) BUG: Fixed a small bug on None condition (#1594) Update deepseg_sc folder --> Add README.txt (#1598) Fixing links to the models. (#1596) DEV: Add Alternative mirror sct_deepseg_gm implementation (#1564) DEV: Modify install_sct to download the deepesg models DEV: rename API folder DEV: changes on the testing function DEV: update OSF link DEV: renaming functions DEV: Correction of the usage.set_description DEV: fill z_holes DEV: modify default features param DEV: NN architecture in spinalcordtoolbox folder DEV: New NN architecture DEV: No need for the prediction ... # Conflicts: # dev/GM_atlas/concatenate_WM_and_GM_tracts.py # dev/GM_atlas/registration_gm_atlas.py # dev/atlas/create_atlas/create_masks_csf_and_gm.py # dev/atlas/validate_atlas/compute_dice.py # dev/atlas/validate_atlas/compute_fractional_volume_per_label.py # dev/atlas/validate_atlas/crop_image.py # dev/atlas/validate_atlas/generate_phantom.py # dev/atlas/validate_atlas/plot_abs_error_vs_csf_values.py # dev/atlas/validate_atlas/plot_abs_error_vs_fractional_volume.py # dev/atlas/validate_atlas/plot_auto_vs_manual.py # dev/atlas/validate_atlas/plot_map.py # dev/atlas/validate_atlas/plot_snr_and_tracts_std.py # dev/atlas/validate_atlas/validate_atlas.py # dev/control_points/make_centerline.py # dev/control_points/process.py # dev/control_points/processjeudi.py # dev/control_points/sct_utils.py # dev/control_points/segall.py # dev/control_points/smoothall.py # dev/control_points/splines_approximation_v2.py # dev/control_points/straighten.py # dev/control_points/test.py # dev/denoise/ornlm/setup.py # dev/generate_ml_data.py # dev/githook/pre_commit_hook.py # dev/itk_transfo/mat_to_displacement.py # dev/sct_detect_spinalcord/sct_detect_spinalcord.py # dev/sct_detect_spinalcord/sct_get_centerline_automatic.py # dev/sct_detect_spinalcord/sct_get_centerline_from_labels.py # dev/sct_dmri_moco__old.py # dev/sct_nin_convert_dcm2nii.py # dev/sct_register_graymatter/sct_register_graymatter.py # dev/sct_register_graymatter/sct_register_graymatter_old.py # dev/sct_register_graymatter/test_sct_register_graymatter.py # dev/sct_register_spine_straightened_to_template.py # dev/sct_register_straight_spinalcord_to_template.py # dev/sct_resample/sct_resample_new.py # dev/sct_resample/sct_resample_old.py # dev/sct_scad.py # dev/sct_segment_gray_matter_asman/2015-07-13_full_scripts_with_Old_unused_functions/sct_segment_graymatter.py # dev/sct_segment_gray_matter_asman/2015-08-17-full_scripts_before_cleaning/sct_segment_graymatter.py # dev/sct_segment_gray_matter_asman/2015-08-17-full_scripts_before_cleaning/sct_segment_graymatter_old.py # dev/sct_smooth_spinal_cord__ISABELLE.py # dev/spinal_level/sct_extract_spinal_levels.py # dev/straightening/optimize_straightening.py # dev/straightening/sct_straighten_spinalcord_LargeFOVOutput.py # dev/tamag/copydiffe.py # dev/tamag/create_generation_info_files.py # dev/tamag/make_warp_null.py # dev/tamag/old/add_noise.py # dev/tamag/old/create_line_on_slice.py # dev/tamag/old/curveSmoothing.py # dev/tamag/old/extract_sagitale.py # dev/tamag/old/get_warping_field.py # dev/tamag/old/msct_get_centerline_from_labels.py # dev/tamag/old/msct_register_reg.py # dev/tamag/old/pipeline_marseille.py # dev/tamag/old/pipeline_preprocessing.py # dev/tamag/old/pipeline_preprocessing_T1.py # dev/tamag/old/pipeline_preprocessing_after_segmentation.py # dev/tamag/old/pipeline_segmentation_T2.py # dev/tamag/old/pipeline_template.py # dev/tamag/old/pipeline_template_T1.py # dev/tamag/old/pipeline_template_T1_from_T2.py # dev/tamag/old/preprocess_data_T1.py # dev/tamag/old/preprocess_data_T2.py # dev/tamag/old/rename_all.py # dev/tamag/old/sct_addlabel.py # dev/tamag/old/sct_denoising_nlm.py # dev/tamag/old/sct_denoizing_nlm.py # dev/tamag/old/sct_function_preprocessing.py # dev/tamag/old/sct_get_centerline_from_labels2.py # dev/tamag/old/test_class_extract_cent.py # dev/tamag/old/test_denoizing_dipy.py # dev/tamag/old/test_filtering.py # dev/tamag/rename_all.py # dev/tamag/test_msct_image.py # dev/tamag/test_msct_register # dev/tamag/test_msct_register.py # dev/tamag/test_register_landmarks_for_images.py # dev/template/pipeline_template_2.py # dev/template_creation/sct_average_levels.py # dev/template_creation/sct_change_file_type.py # dev/template_creation/sct_generate_centerline.py # dev/template_creation/sct_normalize.py # dev/template_creation/sct_push_into_template_space.py # dev/template_creation/sct_symetrize.py # dev/template_creation/sct_template_crop_data.py # dev/template_preprocessing/README.md # dev/wt_scripts/sct_icv_RBM.py # dev/wt_scripts/sct_manage_dicom.py
jcohenadad
added a commit
that referenced
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Dec 18, 2019
* jca-release: (88 commits) updated CHANGES.md Adding minimal Dockerfile for SCT. (#1600) Added a study in SCT applications section Fix TensorFlow installation on Debian (#1601) BUG: Fixed a small bug on None condition (#1594) Update deepseg_sc folder --> Add README.txt (#1598) Fixing links to the models. (#1596) DEV: Add Alternative mirror sct_deepseg_gm implementation (#1564) DEV: Modify install_sct to download the deepesg models DEV: rename API folder DEV: changes on the testing function DEV: update OSF link DEV: renaming functions DEV: Correction of the usage.set_description DEV: fill z_holes DEV: modify default features param DEV: NN architecture in spinalcordtoolbox folder DEV: New NN architecture DEV: No need for the prediction ... # Conflicts: # dev/GM_atlas/concatenate_WM_and_GM_tracts.py # dev/GM_atlas/registration_gm_atlas.py # dev/atlas/create_atlas/create_masks_csf_and_gm.py # dev/atlas/validate_atlas/compute_dice.py # dev/atlas/validate_atlas/compute_fractional_volume_per_label.py # dev/atlas/validate_atlas/crop_image.py # dev/atlas/validate_atlas/generate_phantom.py # dev/atlas/validate_atlas/plot_abs_error_vs_csf_values.py # dev/atlas/validate_atlas/plot_abs_error_vs_fractional_volume.py # dev/atlas/validate_atlas/plot_auto_vs_manual.py # dev/atlas/validate_atlas/plot_map.py # dev/atlas/validate_atlas/plot_snr_and_tracts_std.py # dev/atlas/validate_atlas/validate_atlas.py # dev/control_points/make_centerline.py # dev/control_points/process.py # dev/control_points/processjeudi.py # dev/control_points/sct_utils.py # dev/control_points/segall.py # dev/control_points/smoothall.py # dev/control_points/splines_approximation_v2.py # dev/control_points/straighten.py # dev/control_points/test.py # dev/denoise/ornlm/setup.py # dev/generate_ml_data.py # dev/githook/pre_commit_hook.py # dev/itk_transfo/mat_to_displacement.py # dev/sct_detect_spinalcord/sct_detect_spinalcord.py # dev/sct_detect_spinalcord/sct_get_centerline_automatic.py # dev/sct_detect_spinalcord/sct_get_centerline_from_labels.py # dev/sct_dmri_moco__old.py # dev/sct_nin_convert_dcm2nii.py # dev/sct_register_graymatter/sct_register_graymatter.py # dev/sct_register_graymatter/sct_register_graymatter_old.py # dev/sct_register_graymatter/test_sct_register_graymatter.py # dev/sct_register_spine_straightened_to_template.py # dev/sct_register_straight_spinalcord_to_template.py # dev/sct_resample/sct_resample_new.py # dev/sct_resample/sct_resample_old.py # dev/sct_scad.py # dev/sct_segment_gray_matter_asman/2015-07-13_full_scripts_with_Old_unused_functions/sct_segment_graymatter.py # dev/sct_segment_gray_matter_asman/2015-08-17-full_scripts_before_cleaning/sct_segment_graymatter.py # dev/sct_segment_gray_matter_asman/2015-08-17-full_scripts_before_cleaning/sct_segment_graymatter_old.py # dev/sct_smooth_spinal_cord__ISABELLE.py # dev/spinal_level/sct_extract_spinal_levels.py # dev/straightening/optimize_straightening.py # dev/straightening/sct_straighten_spinalcord_LargeFOVOutput.py # dev/tamag/copydiffe.py # dev/tamag/create_generation_info_files.py # dev/tamag/make_warp_null.py # dev/tamag/old/add_noise.py # dev/tamag/old/create_line_on_slice.py # dev/tamag/old/curveSmoothing.py # dev/tamag/old/extract_sagitale.py # dev/tamag/old/get_warping_field.py # dev/tamag/old/msct_get_centerline_from_labels.py # dev/tamag/old/msct_register_reg.py # dev/tamag/old/pipeline_marseille.py # dev/tamag/old/pipeline_preprocessing.py # dev/tamag/old/pipeline_preprocessing_T1.py # dev/tamag/old/pipeline_preprocessing_after_segmentation.py # dev/tamag/old/pipeline_segmentation_T2.py # dev/tamag/old/pipeline_template.py # dev/tamag/old/pipeline_template_T1.py # dev/tamag/old/pipeline_template_T1_from_T2.py # dev/tamag/old/preprocess_data_T1.py # dev/tamag/old/preprocess_data_T2.py # dev/tamag/old/rename_all.py # dev/tamag/old/sct_addlabel.py # dev/tamag/old/sct_denoising_nlm.py # dev/tamag/old/sct_denoizing_nlm.py # dev/tamag/old/sct_function_preprocessing.py # dev/tamag/old/sct_get_centerline_from_labels2.py # dev/tamag/old/test_class_extract_cent.py # dev/tamag/old/test_denoizing_dipy.py # dev/tamag/old/test_filtering.py # dev/tamag/rename_all.py # dev/tamag/test_msct_image.py # dev/tamag/test_msct_register # dev/tamag/test_msct_register.py # dev/tamag/test_register_landmarks_for_images.py # dev/template/pipeline_template_2.py # dev/template_creation/sct_average_levels.py # dev/template_creation/sct_change_file_type.py # dev/template_creation/sct_generate_centerline.py # dev/template_creation/sct_normalize.py # dev/template_creation/sct_push_into_template_space.py # dev/template_creation/sct_symetrize.py # dev/template_creation/sct_template_crop_data.py # dev/template_preprocessing/README.md # dev/wt_scripts/sct_icv_RBM.py # dev/wt_scripts/sct_manage_dicom.py Former-commit-id: f709a6f
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Minimal Dockerfile for SCT w/ Ubuntu 16.04
This is just a minimal Dockerfile for SCT w/ Ubuntu 16.04. I made for myself but it might be useful for other people when they cannot run SCT on their platform.