create isolated conda envs and integrate them with snakemake rules

khanlab · Jan 10, 2025 · 0dbe1f9 · 0dbe1f9
1 parent e3a861d
commit 0dbe1f9
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diff --git a/hippunfold/workflow/envs/env1.yaml b/hippunfold/workflow/envs/env1.yaml
@@ -0,0 +1,22 @@
+name: env1
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - batchgenerators
+# - nnunet-inference-on-cpu-and-gpu = "1.6.6" 
+  - numpy=1.21.2
+  - astropy>=4.0,<4.3.1
+  - pandas>=1.2.0,<1.3.0
+  - nibabel>=3.2.1
+  - scipy=1.7.1
+  - nilearn>=0.8.1
+  - seaborn>=0.11.2
+  - scikit-fmm>=2022.03.26
+  - simpleitk=2.0.2
+  - matplotlib=3.4.2
+  - pytorch=1.10.0
+  - pyvista>=0.44.2
+  - naturalneighbor>=0.2.1
+  - vtk
diff --git a/hippunfold/workflow/envs/env2.yaml b/hippunfold/workflow/envs/env2.yaml
@@ -0,0 +1,7 @@
+name: env2
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - convert3d
diff --git a/hippunfold/workflow/envs/env3.yaml b/hippunfold/workflow/envs/env3.yaml
@@ -0,0 +1,7 @@
+name: env3
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - connectome-workbench
diff --git a/hippunfold/workflow/envs/env4.yaml b/hippunfold/workflow/envs/env4.yaml
@@ -0,0 +1,7 @@
+name: env4
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - ants=2.5.4
diff --git a/hippunfold/workflow/envs/env5.yaml b/hippunfold/workflow/envs/env5.yaml
@@ -0,0 +1,7 @@
+name: env5
+channels:
+  - khanlab
+  - defaults
+dependencies:
+  - python=3.9
+  - greedyreg
diff --git a/hippunfold/workflow/envs/env6.yaml b/hippunfold/workflow/envs/env6.yaml
@@ -0,0 +1,7 @@
+name: env6
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - niftyreg
diff --git a/hippunfold/workflow/envs/env7.yaml b/hippunfold/workflow/envs/env7.yaml
@@ -0,0 +1,8 @@
+name: env6
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - niftyreg
+  - convert3d
diff --git a/hippunfold/workflow/envs/env8.yaml b/hippunfold/workflow/envs/env8.yaml
@@ -0,0 +1,6 @@
+name: env8
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
diff --git a/hippunfold/workflow/rules/autotop.smk b/hippunfold/workflow/rules/autotop.smk
@@ -80,6 +80,8 @@ rule laplace_coords_hipp:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env1.yaml"
     script:
         get_cmd_laplace_coords()
 
@@ -165,6 +167,8 @@ rule prep_equivolume_coords:
         "subj"
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env1.yaml"
     script:
         "../scripts/prep_equivolume_coords.py"
 

diff --git a/hippunfold/workflow/rules/download.smk b/hippunfold/workflow/rules/download.smk
@@ -81,6 +81,8 @@ rule import_template_dseg:
         "subj"
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     shell:
         "{params.copy_or_flip_cmd} {output.template_seg}"
 
@@ -120,6 +122,8 @@ rule import_template_coords:
         "subj"
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     shell:
         "{params.copy_or_flip_cmd} {output.template_coords}"
 
@@ -158,5 +162,7 @@ rule import_template_anat:
         "subj"
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     shell:
         "{params.copy_or_flip_cmd} {output.template_anat}"
diff --git a/hippunfold/workflow/rules/gifti.smk b/hippunfold/workflow/rules/gifti.smk
@@ -34,6 +34,8 @@ rule cp_template_to_unfold:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     shell:
@@ -73,6 +75,8 @@ rule calc_unfold_template_coords:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     shadow:
         "minimal"  #this is required to use the temporary files defined as params
     group:
@@ -138,6 +142,8 @@ rule constrain_surf_to_bbox:
         "subj"
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env1.yaml"
     script:
         "../scripts/constrain_surf_to_bbox.py"
 
@@ -190,6 +196,8 @@ rule warp_gii_unfold2corobl1:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     shell:
@@ -234,6 +242,8 @@ rule correct_bad_vertices1:
         "subj"
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env1.yaml"
     script:
         "../scripts/fillbadvertices.py"
 
@@ -266,6 +276,8 @@ rule calculate_surface_area1:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     shell:
@@ -319,6 +331,8 @@ rule calculate_gyrification1:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     shell:
@@ -354,6 +368,8 @@ rule calculate_curvature_from_surface1:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     shell:
@@ -390,6 +406,8 @@ rule normalize_curvature1:
         "subj"
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env1.yaml"
     script:
         "../scripts/normalize_tanh.py"
 
@@ -432,6 +450,8 @@ rule calculate_thickness_from_surface1:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     shell:
@@ -486,6 +506,8 @@ rule metric_to_nii:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     shell:
@@ -568,6 +590,8 @@ rule unfolded_registration:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env4.yaml"
     group:
         "subj"
     log:
@@ -640,6 +664,8 @@ rule warp_gii_unfoldreg:
         "subj"
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env1.yaml"
     script:
         "../scripts/warp_flatsurf.py"
 
@@ -743,6 +769,8 @@ rule warp_gii_unfold2corobl2:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     shell:
@@ -785,6 +813,8 @@ rule correct_bad_vertices2:
         "subj"
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env1.yaml"
     script:
         "../scripts/fillbadvertices.py"
 
@@ -857,6 +887,8 @@ rule affine_gii_to_native:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     shell:
@@ -889,6 +921,8 @@ rule calculate_surface_area2:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     shell:
@@ -939,6 +973,8 @@ rule calculate_gyrification2:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     shell:
@@ -972,6 +1008,8 @@ rule calculate_curvature_from_surface2:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     shell:
@@ -1006,6 +1044,8 @@ rule normalize_curvature2:
         "subj"
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env1.yaml"
     script:
         "../scripts/normalize_tanh.py"
 
@@ -1045,6 +1085,8 @@ rule calculate_thickness_from_surface2:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     shell:
@@ -1092,6 +1134,8 @@ rule resample_atlas_to_refvol:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env4.yaml"
     group:
         "subj"
     shell:
@@ -1138,6 +1182,8 @@ rule nii_to_label_gii:
         "subj"
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     shadow:
         "minimal"
     shell:
@@ -1203,6 +1249,8 @@ rule create_dscalar_metric_cifti:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     shell:
@@ -1269,6 +1317,8 @@ rule create_dlabel_cifti_subfields:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     shell:
@@ -1413,6 +1463,8 @@ rule create_spec_file_hipp:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     shell:
@@ -1478,6 +1530,8 @@ rule create_spec_file_dentate:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     shell:
@@ -1512,6 +1566,8 @@ rule merge_lr_spec_file:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     shell: