[cloud] Update cloud toolbox (#836)

galaxyproject · Sep 11, 2024 · 49b7689 · 49b7689
1 parent 263283c
commit 49b7689
Show file tree

Hide file tree

Showing 30 changed files with 261 additions and 39 deletions.
diff --git a/cloud/assembly.yml b/cloud/assembly.yml
@@ -8,3 +8,5 @@ tools:
   owner: iuc
 - name: racon
   owner: bgruening
+- name: gfastats
+  owner: bgruening
diff --git a/cloud/assembly.yml.lock b/cloud/assembly.yml.lock
@@ -7,6 +7,7 @@ tools:
   owner: iuc
   revisions:
   - 9e3e80cc4ad4
+  - e022dff952df
   tool_panel_section_id: assembly
   tool_panel_section_label: Assembly
 - name: spades
@@ -19,11 +20,19 @@ tools:
   owner: iuc
   revisions:
   - 8dee0218ac7d
+  - b799a615995d
   tool_panel_section_id: assembly
   tool_panel_section_label: Assembly
 - name: racon
   owner: bgruening
   revisions:
+  - 78c533842eeb
   - a199cd7ac344
   tool_panel_section_id: assembly
   tool_panel_section_label: Assembly
+- name: gfastats
+  owner: bgruening
+  revisions:
+  - 3ef480892a9f
+  tool_panel_section_id: assembly
+  tool_panel_section_label: Assembly
diff --git a/cloud/bed.yml.lock b/cloud/bed.yml.lock
@@ -6,7 +6,8 @@ tools:
 - name: bedtools
   owner: iuc
   revisions:
-  - ce3c7f062223
   - 07e8b80f278c
+  - 64e2edfe7a2c
+  - ce3c7f062223
   tool_panel_section_id: bed
   tool_panel_section_label: BED
diff --git a/cloud/collection_operations.yml b/cloud/collection_operations.yml
@@ -8,3 +8,5 @@ tools:
   owner: iuc
 - name: collection_column_join
   owner: iuc
+- name: pick_value
+  owner: iuc
diff --git a/cloud/collection_operations.yml.lock b/cloud/collection_operations.yml.lock
@@ -12,6 +12,7 @@ tools:
 - name: split_file_to_collection
   owner: bgruening
   revisions:
+  - 2dae863c8f42
   - 6cbe2f30c2d7
   tool_panel_section_id: collection_operations
   tool_panel_section_label: Collection Operations
@@ -25,6 +26,13 @@ tools:
   owner: iuc
   revisions:
   - 071084070619
+  - 3ddd99c7efee
   - 58228a4d58fe
   tool_panel_section_id: collection_operations
   tool_panel_section_label: Collection Operations
+- name: pick_value
+  owner: iuc
+  revisions:
+  - b19e21af9c52
+  tool_panel_section_id: collection_operations
+  tool_panel_section_label: Collection Operations
diff --git a/cloud/convert_formats.yml.lock b/cloud/convert_formats.yml.lock
@@ -7,4 +7,5 @@ tools:
   owner: iuc
   revisions:
   - b026dae67fba
+  tool_panel_section_id: convert_formats
   tool_panel_section_label: Convert Formats
diff --git a/cloud/datamash.yml.lock b/cloud/datamash.yml.lock
@@ -6,20 +6,23 @@ tools:
 - name: datamash_reverse
   owner: iuc
   revisions:
+  - b8a457820315
   - f198773344e4
   tool_panel_section_id: datamash
   tool_panel_section_label: Datamash
 - name: datamash_transpose
   owner: iuc
   revisions:
+  - 22c2a1ac7ae3
   - 374cb875d38a
+  - a513e3fbb4c5
   - ac092723240d
-  - 22c2a1ac7ae3
   tool_panel_section_id: datamash
   tool_panel_section_label: Datamash
 - name: datamash_ops
   owner: iuc
   revisions:
+  - 4c07ddedc198
   - 746e8e4bf929
   tool_panel_section_id: datamash
   tool_panel_section_label: Datamash
diff --git a/cloud/deeptools.yml.lock b/cloud/deeptools.yml.lock
@@ -7,95 +7,111 @@ tools:
   owner: bgruening
   revisions:
   - 514fa53b5efb
+  - a60c359ec43c
   tool_panel_section_id: deeptools
   tool_panel_section_label: deepTools
 - name: deeptools_plot_heatmap
   owner: bgruening
   revisions:
   - a4dfb122e52b
+  - e4c7985d4585
   tool_panel_section_id: deeptools
   tool_panel_section_label: deepTools
 - name: deeptools_bam_compare
   owner: bgruening
   revisions:
+  - c929a006727f
   - e821645ef8fc
   tool_panel_section_id: deeptools
   tool_panel_section_label: deepTools
 - name: deeptools_bam_pe_fragmentsize
   owner: bgruening
   revisions:
   - 62eb6d63f582
+  - c06951d10364
   tool_panel_section_id: deeptools
   tool_panel_section_label: deepTools
 - name: deeptools_bigwig_compare
   owner: bgruening
   revisions:
+  - 07418a30ed01
   - 26e7304d6737
   tool_panel_section_id: deeptools
   tool_panel_section_label: deepTools
 - name: deeptools_compute_gc_bias
   owner: bgruening
   revisions:
+  - 26983857c91a
   - 2bc10a9ca58b
   tool_panel_section_id: deeptools
   tool_panel_section_label: deepTools
 - name: deeptools_correct_gc_bias
   owner: bgruening
   revisions:
   - 2c37ce318bc3
+  - e479c7ca5570
   tool_panel_section_id: deeptools
   tool_panel_section_label: deepTools
 - name: deeptools_multi_bam_summary
   owner: bgruening
   revisions:
+  - 01fb6a7654e6
   - 78f405266706
   tool_panel_section_id: deeptools
   tool_panel_section_label: deepTools
 - name: deeptools_multi_bigwig_summary
   owner: bgruening
   revisions:
+  - 137c4beed34b
   - 3c9f0c486cca
   tool_panel_section_id: deeptools
   tool_panel_section_label: deepTools
 - name: deeptools_plot_correlation
   owner: bgruening
   revisions:
   - 32e451def88c
+  - bad3ca889618
   tool_panel_section_id: deeptools
   tool_panel_section_label: deepTools
 - name: deeptools_plot_coverage
   owner: bgruening
   revisions:
+  - 231994413f89
   - 56bce3c82278
   tool_panel_section_id: deeptools
   tool_panel_section_label: deepTools
 - name: deeptools_plot_enrichment
   owner: bgruening
   revisions:
+  - 4431f39ede55
   - e65d16fb2724
   tool_panel_section_id: deeptools
   tool_panel_section_label: deepTools
 - name: deeptools_plot_fingerprint
   owner: bgruening
   revisions:
   - 2da482e408b8
+  - 4ed32329e0ed
   tool_panel_section_id: deeptools
   tool_panel_section_label: deepTools
 - name: deeptools_plot_pca
   owner: bgruening
   revisions:
+  - 443d9a9d6d11
   - 69264da0ce77
   tool_panel_section_id: deeptools
   tool_panel_section_label: deepTools
 - name: deeptools_bam_coverage
   owner: bgruening
   revisions:
+  - 0e49b109abc2
   - bb1e4f63e0e6
   tool_panel_section_id: deeptools
   tool_panel_section_label: deepTools
 - name: deeptools_plot_profile
   owner: bgruening
   revisions:
+  - 6662b1a8d326
   - c361b12d207a
   tool_panel_section_id: deeptools
   tool_panel_section_label: deepTools
diff --git a/cloud/expressiontools.yml.lock b/cloud/expressiontools.yml.lock
@@ -6,10 +6,13 @@ tools:
 - name: map_param_value
   owner: iuc
   revisions:
+  - 5ac8a4bf7a8d
   - a01f088d0e5e
+  tool_panel_section_id: expression_tools
   tool_panel_section_label: Expression Tools
 - name: compose_text_param
   owner: iuc
   revisions:
   - e188c9826e0f
+  tool_panel_section_id: expression_tools
   tool_panel_section_label: Expression Tools
diff --git a/cloud/fasta_fastq.yml.lock b/cloud/fasta_fastq.yml.lock
@@ -8,8 +8,10 @@ tools:
   revisions:
   - 093678460093
   - 135b80fb1ac2
-  - c5e2e5902201
+  - 5eb7e84243f2
   - 660cffd8d92a
+  - aa784cb3810d
+  - c5e2e5902201
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
 - name: fastq_filter
@@ -51,21 +53,23 @@ tools:
 - name: flash
   owner: iuc
   revisions:
+  - 01a4ebf1f237
   - a27654fc4270
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
 - name: trim_galore
   owner: bgruening
   revisions:
   - 084bbd8ba7b8
+  - cd7e644cae1d
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
 - name: umi_tools_count
   owner: iuc
   revisions:
   - 8250ea3a1501
-  - b557acca0b56
   - a535cf1e5da4
+  - b557acca0b56
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
 - name: umi_tools_extract

diff --git a/cloud/fastq_quality_control.yml.lock b/cloud/fastq_quality_control.yml.lock
@@ -6,27 +6,30 @@ tools:
 - name: multiqc
   owner: iuc
   revisions:
+  - 1c2db0054039
+  - 5e33b465d8d5
   - 75c93c70d094
   - 9a913cdee30e
-  - df99138d2776
   - abfd8a6544d7
-  - 5e33b465d8d5
-  - 1c2db0054039
+  - df99138d2776
+  - f7e2f1eb3a16
   tool_panel_section_id: fastq_quality_control
   tool_panel_section_label: FASTQ Quality Control
 - name: fastp
   owner: iuc
   revisions:
   - 65b93b623c77
+  - d60c3f704da0
   - dbf9c561ef29
   tool_panel_section_id: fastq_quality_control
   tool_panel_section_label: FASTQ Quality Control
 - name: fastqc
   owner: devteam
   revisions:
+  - 2c64fded1286
   - 3d0c7bdf12f5
-  - e7b2202befea
   - 9da02be9c6cc
+  - e7b2202befea
   tool_panel_section_id: fastq_quality_control
   tool_panel_section_label: FASTQ Quality Control
 - name: trimmomatic

diff --git a/cloud/gemini.yml.lock b/cloud/gemini.yml.lock
@@ -8,16 +8,19 @@ tools:
   revisions:
   - 2270a8b83c12
   - cf61daf064fe
+  tool_panel_section_id: gemini
   tool_panel_section_label: GEMINI
 - name: gemini_db_info
   owner: iuc
   revisions:
-  - c2a413e47fe9
   - 4c5f4e9b1931
+  - c2a413e47fe9
+  tool_panel_section_id: gemini
   tool_panel_section_label: GEMINI
 - name: gemini_query
   owner: iuc
   revisions:
-  - 77a1e60fd1de
   - 666f60a9331a
+  - 77a1e60fd1de
+  tool_panel_section_id: gemini
   tool_panel_section_label: GEMINI
diff --git a/cloud/get_data.yml.lock b/cloud/get_data.yml.lock
@@ -7,11 +7,13 @@ tools:
   owner: iuc
   revisions:
   - 83c7d564b128
+  - 8848455c0270
   tool_panel_section_id: get_data
   tool_panel_section_label: Get Data
 - name: ncbi_acc_download
   owner: iuc
   revisions:
   - 1c58de56d587
+  - e063168e0a81
   tool_panel_section_id: get_data
   tool_panel_section_label: Get Data
diff --git a/cloud/graph_display_data.yml.lock b/cloud/graph_display_data.yml.lock
@@ -7,12 +7,14 @@ tools:
   owner: iuc
   revisions:
   - 2824d77cd8f8
+  - 36b848d5f3ec
   tool_panel_section_id: graph_display_data
   tool_panel_section_label: Graph/Display Data
 - name: circos
   owner: iuc
   revisions:
   - df7356989ac1
+  - c4bde687c846
   tool_panel_section_id: graph_display_data
   tool_panel_section_label: Graph/Display Data
 - name: jbrowse
@@ -27,6 +29,7 @@ tools:
   revisions:
   - 83c573f2e73c
   - 73b8cb5bddcd
+  - 2f557f6abbfb
   tool_panel_section_id: graph_display_data
   tool_panel_section_label: Graph/Display Data
 - name: pathview
@@ -42,5 +45,6 @@ tools:
   - 53460afd5115
   - 566197475670
   - 4955e9bb96d1
+  - 374e9062d874
   tool_panel_section_id: graph_display_data
   tool_panel_section_label: Graph/Display Data
diff --git a/cloud/machine_learning.yml.lock b/cloud/machine_learning.yml.lock
@@ -1,4 +1,4 @@
-install_repository_dependencies: true
+install_repository_dependencies: false
 install_resolver_dependencies: false
 install_tool_dependencies: false
 tool_panel_section_label: Machine Learning