Install IWC tools for galaxy-qa1.galaxy.cloud.e-infra.cz

galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml

@@ -138,3 +138,31 @@ tools:
   owner: iuc
 - name: funannotate_sort
   owner: iuc
+- name: staramr
+  owner: iuc
+- name: amrfinderplus
+  owner: iuc
+- name: isescan
+  owner: iuc
+- name: integron_finder
+  owner: iuc
+- name: bakta
+  owner: iuc
+- name: repeatmodeler
+  owner: csbl
+- name: prodigal
+  owner: iuc
+- name: argnorm
+  owner: iuc
+- name: mmseqs2_taxonomy_assignment
+  owner: iuc
+- name: busco
+  owner: iuc
+- name: ncbi_fcs_adaptor
+  owner: richard-burhans
+- name: compleasm
+  owner: iuc
+- name: helixer
+  owner: genouest
+- name: omark
+  owner: iuc

galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml.lock

@@ -1,4 +1,4 @@
-install_repository_dependencies: true
+install_repository_dependencies: false
 install_resolver_dependencies: false
 install_tool_dependencies: false
 tools:
@@ -144,6 +144,7 @@ tools:
 - name: abricate
   owner: iuc
   revisions:
+  - 3f3e247c053d
   - c2ef298da409
   tool_panel_section_id: annotation
   tool_panel_section_label: Annotation
@@ -162,6 +163,9 @@ tools:
 - name: column_maker
   owner: devteam
   revisions:
+  - 02026300aa45
+  - 427903d47026
+  - 6595517c2dd8
   - 9cd341095afd
   - aff5135563c6
   tool_panel_section_id: annotation
@@ -431,3 +435,91 @@ tools:
   - d77fdcca400e
   tool_panel_section_id: annotation
   tool_panel_section_label: Annotation
+- name: staramr
+  owner: iuc
+  revisions:
+  - 6d5c8a6ceea0
+  - eaa563bd535a
+  tool_panel_section_id: annotation
+  tool_panel_section_label: Annotation
+- name: amrfinderplus
+  owner: iuc
+  revisions:
+  - 7844dbe4f8e2
+  tool_panel_section_id: annotation
+  tool_panel_section_label: Annotation
+- name: isescan
+  owner: iuc
+  revisions:
+  - 81539b9ae80a
+  tool_panel_section_id: annotation
+  tool_panel_section_label: Annotation
+- name: integron_finder
+  owner: iuc
+  revisions:
+  - bfd290fe1588
+  tool_panel_section_id: annotation
+  tool_panel_section_label: Annotation
+- name: bakta
+  owner: iuc
+  revisions:
+  - 1942e86e2ee1
+  tool_panel_section_id: annotation
+  tool_panel_section_label: Annotation
+- name: repeatmodeler
+  owner: csbl
+  revisions:
+  - 4a172d211285
+  - 8661b2607b7e
+  tool_panel_section_id: annotation
+  tool_panel_section_label: Annotation
+- name: prodigal
+  owner: iuc
+  revisions:
+  - 91791b6ecd38
+  tool_panel_section_id: annotation
+  tool_panel_section_label: Annotation
+- name: argnorm
+  owner: iuc
+  revisions:
+  - d8e95a03321a
+  tool_panel_section_id: annotation
+  tool_panel_section_label: Annotation
+- name: mmseqs2_taxonomy_assignment
+  owner: iuc
+  revisions:
+  - 876d26806584
+  tool_panel_section_id: annotation
+  tool_panel_section_label: Annotation
+- name: busco
+  owner: iuc
+  revisions:
+  - 2babe6d5c561
+  - 4e70d88adf2f
+  - c5a90fa4b8dd
+  tool_panel_section_id: annotation
+  tool_panel_section_label: Annotation
+- name: ncbi_fcs_adaptor
+  owner: richard-burhans
+  revisions:
+  - d55ad8533d58
+  tool_panel_section_id: annotation
+  tool_panel_section_label: Annotation
+- name: compleasm
+  owner: iuc
+  revisions:
+  - fc7334661489
+  tool_panel_section_id: annotation
+  tool_panel_section_label: Annotation
+- name: helixer
+  owner: genouest
+  revisions:
+  - c2fc4ac35199
+  tool_panel_section_id: annotation
+  tool_panel_section_label: Annotation
+- name: omark
+  owner: iuc
+  revisions:
+  - 0291e0e81551
+  tool_panel_section_id: annotation
+  tool_panel_section_label: Annotation

galaxy-qa1.galaxy.cloud.e-infra.cz/assembly.yml

@@ -84,3 +84,33 @@ tools:
   owner: bgruening
 - name: bellerophon
   owner: iuc
+- name: quast
+  owner: iuc
+- name: megahit
+  owner: iuc
+- name: metaspades
+  owner: nml
+- name: merqury
+  owner: iuc
+- name: meryl_count_kmers
+  owner: iuc
+- name: meryl_groups_kmers
+  owner: iuc
+- name: meryl_histogram_kmers
+  owner: iuc
+- name: hifiasm
+  owner: bgruening
+- name: pretext_map
+  owner: iuc
+- name: pretext_graph
+  owner: iuc
+- name: genomescope
+  owner: iuc
+- name: yahs
+  owner: iuc
+- name: pairtools_parse
+  owner: iuc
+- name: pairtools_dedup
+  owner: iuc
+- name: racon
+  owner: bgruening

galaxy-qa1.galaxy.cloud.e-infra.cz/assembly.yml.lock

@@ -1,4 +1,4 @@
-install_repository_dependencies: true
+install_repository_dependencies: false
 install_resolver_dependencies: false
 install_tool_dependencies: false
 tools:
@@ -25,6 +25,7 @@ tools:
   owner: bgruening
   revisions:
   - 99ddbf037d98
+  - bfab6f5b449d
   tool_panel_section_id: assembly
   tool_panel_section_label: Assembly
 - name: mitobim
@@ -205,8 +206,10 @@ tools:
   owner: bgruening
   revisions:
   - 0393c0415171
+  - 3ef480892a9f
   - 50b6ec4074f4
   - 5799092ffdff
+  - 59150c883ed5
   tool_panel_section_id: assembly
   tool_panel_section_label: Assembly
 - name: velvet
@@ -264,3 +267,101 @@ tools:
   - 321347bd0494
   tool_panel_section_id: assembly
   tool_panel_section_label: Assembly
+- name: quast
+  owner: iuc
+  revisions:
+  - 1b1cf0c96501
+  - a3b35edea53a
+  tool_panel_section_id: assembly
+  tool_panel_section_label: Assembly
+- name: megahit
+  owner: iuc
+  revisions:
+  - ab208c87d973
+  tool_panel_section_id: assembly
+  tool_panel_section_label: Assembly
+- name: metaspades
+  owner: nml
+  revisions:
+  - f192c2fbe13f
+  tool_panel_section_id: assembly
+  tool_panel_section_label: Assembly
+- name: merqury
+  owner: iuc
+  revisions:
+  - eb7b00ec347d
+  tool_panel_section_id: assembly
+  tool_panel_section_label: Assembly
+- name: meryl_count_kmers
+  owner: iuc
+  revisions:
+  - bb6774c6aeaf
+  - e893b7452150
+  tool_panel_section_id: assembly
+  tool_panel_section_label: Assembly
+- name: meryl_groups_kmers
+  owner: iuc
+  revisions:
+  - c4758f3bf36e
+  - cc8029eca6e9
+  tool_panel_section_id: assembly
+  tool_panel_section_label: Assembly
+- name: meryl_histogram_kmers
+  owner: iuc
+  revisions:
+  - 9a0227fa7521
+  - fa86bf923473
+  tool_panel_section_id: assembly
+  tool_panel_section_label: Assembly
+- name: hifiasm
+  owner: bgruening
+  revisions:
+  - 5d365d5cbe9d
+  tool_panel_section_id: assembly
+  tool_panel_section_label: Assembly
+- name: pretext_map
+  owner: iuc
+  revisions:
+  - 0346286a3b0a
+  - 9c942221e135
+  - c6cec5ab35c1
+  tool_panel_section_id: assembly
+  tool_panel_section_label: Assembly
+- name: pretext_graph
+  owner: iuc
+  revisions:
+  - 36ce83a739f2
+  - 408ece2e4647
+  tool_panel_section_id: assembly
+  tool_panel_section_label: Assembly
+- name: genomescope
+  owner: iuc
+  revisions:
+  - 460fad600dce
+  tool_panel_section_id: assembly
+  tool_panel_section_label: Assembly
+- name: yahs
+  owner: iuc
+  revisions:
+  - 6756b34312cd
+  tool_panel_section_id: assembly
+  tool_panel_section_label: Assembly
+- name: pairtools_parse
+  owner: iuc
+  revisions:
+  - a5876cca7b05
+  tool_panel_section_id: assembly
+  tool_panel_section_label: Assembly
+- name: pairtools_dedup
+  owner: iuc
+  revisions:
+  - 3d1d241ceff2
+  tool_panel_section_id: assembly
+  tool_panel_section_label: Assembly
+- name: racon
+  owner: bgruening
+  revisions:
+  - 78c533842eeb
+  - e100a765370e
+  tool_panel_section_id: assembly
+  tool_panel_section_label: Assembly

galaxy-qa1.galaxy.cloud.e-infra.cz/bed.yml.lock

@@ -1,11 +1,14 @@
-install_repository_dependencies: true
+install_repository_dependencies: false
 install_resolver_dependencies: false
 install_tool_dependencies: false
 tools:
 - name: bedtools
   owner: iuc
   revisions:
   - 2892111d91f8
+  - 64e2edfe7a2c
+  - a1a923cd89e8
+  - a68aa6c1204a
   - b8348686a0b9
   - dde39ba9c031
   tool_panel_section_id: bed

galaxy-qa1.galaxy.cloud.e-infra.cz/biodiversity_data_exploration.yml.lock

@@ -1,4 +1,4 @@
-install_repository_dependencies: true
+install_repository_dependencies: false
 install_resolver_dependencies: false
 install_tool_dependencies: false
 tools:

galaxy-qa1.galaxy.cloud.e-infra.cz/chemicaltoolbox.yml

@@ -212,3 +212,11 @@ tools:
   owner: chemteam
 - name: gmx_rmsf
   owner: chemteam
+- name: openbabel_compound_convert
+  owner: bgruening
+- name: qcxms_neutral_run
+  owner: recetox
+- name: qcxms_production_run
+  owner: recetox
+- name: qcxms_getres
+  owner: recetox