Merge pull request #901 from mvdbeek/installing_missing_tools_multipl…

…ex_tissue_imaging Install tools for multiplex-tissue-imaging-TMA workflow on test
galaxyproject · Jan 6, 2025 · acddee8 · acddee8
2 parents f232aa3 + 8200006
commit acddee8
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Showing 12 changed files with 94 additions and 44 deletions.
diff --git a/test.galaxyproject.org/chip_seq.yml.lock b/test.galaxyproject.org/chip_seq.yml.lock
@@ -1,4 +1,4 @@
-install_repository_dependencies: false
+install_repository_dependencies: true
 install_resolver_dependencies: false
 install_tool_dependencies: false
 tool_panel_section_label: ChIP-seq
@@ -19,8 +19,8 @@ tools:
 - name: macs2
   owner: iuc
   revisions:
-  - 644444825ef9
   - 1ac88e46ee0f
+  - 644444825ef9
   tool_panel_section_id: chip_seq
   tool_panel_section_label: ChIP-seq
   tool_shed_url: testtoolshed.g2.bx.psu.edu

diff --git a/test.galaxyproject.org/data_managers.yml.lock b/test.galaxyproject.org/data_managers.yml.lock
@@ -12,10 +12,10 @@ tools:
 - name: data_manager_selection_background
   owner: iuc
   revisions:
-  - 10ac95ec81d9
-  - e4f07770b340
   - 0bd1cd5eac51
+  - 10ac95ec81d9
   - bb5794942b5e
+  - e4f07770b340
   tool_panel_section_id: data_managers
   tool_panel_section_label: Data Managers
 - name: data_manager_build_kraken2_database

diff --git a/test.galaxyproject.org/du_novo.yml.lock b/test.galaxyproject.org/du_novo.yml.lock
@@ -1,4 +1,4 @@
-install_repository_dependencies: false
+install_repository_dependencies: true
 install_resolver_dependencies: false
 install_tool_dependencies: false
 tool_panel_section_label: Du Novo
@@ -18,8 +18,8 @@ tools:
 - name: sequence_content_trimmer
   owner: nick
   revisions:
-  - 7f170cb06e2e
   - 464aee13e2df
+  - 7f170cb06e2e
   tool_panel_section_id: du_novo
   tool_panel_section_label: Du Novo
 - name: duplex_family_size_distribution

diff --git a/test.galaxyproject.org/fasta_fastq.yml.lock b/test.galaxyproject.org/fasta_fastq.yml.lock
@@ -201,7 +201,7 @@ tools:
 - name: splitfasta
   owner: rnateam
   revisions:
-  - ae4d5733272f
   - 733ca84b21ee
+  - ae4d5733272f
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
diff --git a/test.galaxyproject.org/get_data.yml.lock b/test.galaxyproject.org/get_data.yml.lock
@@ -12,8 +12,8 @@ tools:
 - name: sra_tools
   owner: iuc
   revisions:
-  - f5ea3ce9b9b0
   - 69ebb7f46e45
+  - f5ea3ce9b9b0
   tool_panel_section_id: get_data
   tool_panel_section_label: Get Data
 - name: ncbi_acc_download
@@ -25,8 +25,8 @@ tools:
 - name: ncbi_datasets
   owner: iuc
   revisions:
-  - 48e0814f250a
   - 2753a5786114
+  - 48e0814f250a
   tool_panel_section_id: get_data
   tool_panel_section_label: Get Data
   tool_shed_url: testtoolshed.g2.bx.psu.edu
diff --git a/test.galaxyproject.org/graph_display_data.yml.lock b/test.galaxyproject.org/graph_display_data.yml.lock
@@ -3,14 +3,6 @@ install_resolver_dependencies: false
 install_tool_dependencies: false
 tool_panel_section_label: Graph/Display Data
 tools:
-- name: ml_visualization_ex
-  owner: bgruening
-  revisions:
-  - 09efff9a5765
-  - 14bd6d59650d
-  - 4a229a7ad638
-  tool_panel_section_id: graph_display_data
-  tool_panel_section_label: Graph/Display Data
 - name: plotly_parallel_coordinates_plot
   owner: bgruening
   revisions:
@@ -176,8 +168,8 @@ tools:
 - name: intervene
   owner: iuc
   revisions:
-  - f5fa293605ca
   - 08780101bc36
+  - f5fa293605ca
   tool_panel_section_id: graph_display_data
   tool_panel_section_label: Graph/Display Data
 - name: jvarkit_wgscoverageplotter

diff --git a/test.galaxyproject.org/machine_learning.yml.lock b/test.galaxyproject.org/machine_learning.yml.lock
@@ -6,37 +6,37 @@ tools:
 - name: model_prediction
   owner: bgruening
   revisions:
+  - 1e088aa741eb
   - 22f9cbcf1582
   - 60c726f5cc5e
   - 6efb9bc6bf32
-  - 1e088aa741eb
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: keras_model_config
   owner: bgruening
   revisions:
   - 0c933465d70e
+  - 2b8d85927742
   - 64bbfa592868
   - c3813c64d678
-  - 2b8d85927742
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: keras_model_builder
   owner: bgruening
   revisions:
+  - 5b35833076f0
   - 9b6faa256f15
   - e3b420d0b71a
   - ed7c222e47e3
-  - 5b35833076f0
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: keras_batch_models
   owner: bgruening
   revisions:
   - 4a5266c96889
   - 62b85c8ad8fa
-  - f5e7df4f7975
   - 77c04469e8b8
+  - f5e7df4f7975
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: sklearn_stacking_ensemble_models
@@ -52,27 +52,27 @@ tools:
   owner: bgruening
   revisions:
   - 2b8406e74f9e
+  - 443471b0a27a
   - a9e0b963b7bb
   - caf7d2b71a48
-  - 443471b0a27a
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: sklearn_estimator_attributes
   owner: bgruening
   revisions:
+  - 5ae00d2908f2
   - 74de84506e74
   - 7a9a9349eb42
   - c9ddd20d25d0
-  - 5ae00d2908f2
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: sklearn_model_validation
   owner: bgruening
   revisions:
   - 4b359039f09f
+  - 65f18ab91132
   - a5aed87b2cc0
   - de360b57a5ab
-  - 65f18ab91132
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: sklearn_svm_classifier
@@ -88,9 +88,9 @@ tools:
   owner: bgruening
   revisions:
   - 0f460421b212
+  - 1fe020b2108f
   - 999e07f0a9fa
   - df579b31311d
-  - 1fe020b2108f
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: sklearn_searchcv
@@ -106,45 +106,45 @@ tools:
   owner: bgruening
   revisions:
   - 0c74d3164ac8
+  - 3f25f37ee3db
   - 3f3c6dc38f3e
   - 664666bd14ec
-  - 3f25f37ee3db
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: sklearn_pairwise_metrics
   owner: bgruening
   revisions:
   - 09bfbef3dd90
+  - 2a1afd3481ce
   - bc17040617c0
   - cd4328a02798
-  - 2a1afd3481ce
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: sklearn_nn_classifier
   owner: bgruening
   revisions:
+  - 309cc7c6af56
   - 34d31bd995e9
   - 699024d5c451
   - 823ecc0bce45
-  - 309cc7c6af56
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: sklearn_numeric_clustering
   owner: bgruening
   revisions:
   - 73e7f1c76ece
   - 83938131dd46
-  - e7f047a9dca9
   - e13a7c05b3a4
+  - e7f047a9dca9
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: sklearn_ensemble
   owner: bgruening
   revisions:
+  - 407495139a09
   - 4ecc0ce9d0a2
   - a98fdfcd9f5f
   - af0523c606a7
-  - 407495139a09
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: sklearn_feature_selection
@@ -160,9 +160,9 @@ tools:
   owner: bgruening
   revisions:
   - 1bef885255e0
+  - add3c3a7c2b4
   - b75cae00f980
   - eb79bde99328
-  - add3c3a7c2b4
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: sklearn_clf_metrics
@@ -177,19 +177,19 @@ tools:
 - name: sklearn_regression_metrics
   owner: bgruening
   revisions:
+  - 6000c1589f33
   - 70c5a9127f99
   - 9c8ede554b7c
   - a152c1d23379
-  - 6000c1589f33
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: sklearn_discriminant_classifier
   owner: bgruening
   revisions:
+  - 1bd039aca44f
   - 420a4bf99244
   - 64b771b1471a
   - e76f6dfea5c9
-  - 1bd039aca44f
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: sklearn_generalized_linear
@@ -213,26 +213,26 @@ tools:
 - name: sklearn_train_test_split
   owner: bgruening
   revisions:
+  - 03611d7232f6
   - 13b9ac5d277c
   - 3312fb686ffb
   - 5a092779412e
-  - 03611d7232f6
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: sklearn_fitted_model_eval
   owner: bgruening
   revisions:
   - 61fb99c55558
+  - c2a7717d96ce
   - cf54bae8ad42
   - e00c1c9d206b
-  - c2a7717d96ce
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: sklearn_to_categorical
   owner: bgruening
   revisions:
-  - f93f0cdbaf18
   - 612ca26c197d
+  - f93f0cdbaf18
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: ml_visualization_ex
@@ -245,8 +245,8 @@ tools:
 - name: sklearn_lightgbm
   owner: bgruening
   revisions:
-  - c48ffc96fe79
   - 74f96ebc5554
+  - c48ffc96fe79
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: sklearn_pca
@@ -259,8 +259,8 @@ tools:
 - name: keras_train_and_eval
   owner: bgruening
   revisions:
-  - ead8f1822587
   - 470aed90aa41
+  - ead8f1822587
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
 - name: scipy_sparse

diff --git a/test.galaxyproject.org/multiple_alignments.yml.lock b/test.galaxyproject.org/multiple_alignments.yml.lock
@@ -12,8 +12,8 @@ tools:
 - name: mafft
   owner: rnateam
   revisions:
-  - c5908940967d
   - aaefa93c2dd2
+  - c5908940967d
   tool_panel_section_id: multiple_alignments
   tool_panel_section_label: Multiple Alignments
 - name: clustalw
@@ -25,8 +25,8 @@ tools:
 - name: kc_align
   owner: iuc
   revisions:
-  - 1c65ddbaeefa
   - 04b13fc809ac
   - 0c0288a9d92c
+  - 1c65ddbaeefa
   tool_panel_section_id: multiple_alignments
   tool_panel_section_label: Multiple Alignments
diff --git a/test.galaxyproject.org/protein_modeling.yml.lock b/test.galaxyproject.org/protein_modeling.yml.lock
@@ -14,8 +14,8 @@ tools:
   owner: guerler
   revisions:
   - 0ea00dce62ab
+  - 75d1aedc9b3f
   - 860bd6f8f480
   - f8ba4dd48cbd
-  - 75d1aedc9b3f
   tool_panel_section_id: protein_modeling
   tool_panel_section_label: Protein Modeling
diff --git a/test.galaxyproject.org/rna_seq.yml.lock b/test.galaxyproject.org/rna_seq.yml.lock
@@ -12,8 +12,8 @@ tools:
 - name: rgrnastar
   owner: iuc
   revisions:
-  - 850f3679b9b4
   - 4074fc1940e2
+  - 850f3679b9b4
   tool_panel_section_id: rna_seq
   tool_panel_section_label: RNA-seq
 - name: hisat2
@@ -73,14 +73,15 @@ tools:
 - name: rnaspades
   owner: iuc
   revisions:
+  - 03fd468e158f
   - 9e58ff014088
   - dd4b53e5b34a
-  - 03fd468e158f
   tool_panel_section_id: rna_seq
   tool_panel_section_label: RNA-seq
 - name: rnaspades
   owner: iuc
   revisions:
+  - 03fd468e158f
   - 9e58ff014088
   - dd4b53e5b34a
   tool_panel_section_id: rna_seq
@@ -128,6 +129,12 @@ tools:
   - 0761bbc0a4e7
   tool_panel_section_id: rna_seq
   tool_panel_section_label: RNA-seq
+- name: cummerbund
+  owner: devteam
+  revisions:
+  - c3b54a4b7741
+  tool_panel_section_id: rna_seq
+  tool_panel_section_label: RNA-seq
 - name: cuffquant
   owner: devteam
   revisions:

diff --git a/test.galaxyproject.org/spatial_omics.yml b/test.galaxyproject.org/spatial_omics.yml
@@ -0,0 +1,12 @@
+tool_panel_section_label: Spatial Omics
+tools:
+- name: basic_illumination
+  owner: perssond
+- name: ashlar
+  owner: perssond
+- name: coreograph
+  owner: perssond
+- name: mesmer
+  owner: goeckslab
+- name: quantification
+  owner: perssond