[cloud] Update cloud toolset (#883)

* Fix fix-no-deps and fix_lockfile for int revisions

* [cloud] Add a few missing tools

* [cloud] Update tools

cloud/assembly.yml

@@ -10,3 +10,5 @@ tools:
   owner: bgruening
 - name: gfastats
   owner: bgruening
+- name: quast
+  owner: iuc

cloud/assembly.yml.lock

@@ -14,6 +14,7 @@ tools:
   owner: nml
   revisions:
   - b8c00ce5dfa0
+  - d5887ace0dd4
   tool_panel_section_id: assembly
   tool_panel_section_label: Assembly
 - name: miniasm
@@ -34,5 +35,12 @@ tools:
   owner: bgruening
   revisions:
   - 3ef480892a9f
+  - f4a3eff8ab85
+  tool_panel_section_id: assembly
+  tool_panel_section_label: Assembly
+- name: quast
+  owner: iuc
+  revisions:
+  - 72472698a2df
   tool_panel_section_id: assembly
   tool_panel_section_label: Assembly

cloud/fasta_fastq.yml.lock

@@ -17,37 +17,43 @@ tools:
 - name: fastq_filter
   owner: devteam
   revisions:
+  - '144275714590'
   - 81a9090d6df3
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
 - name: fastq_groomer
   owner: devteam
   revisions:
   - 47e5dbc3e790
+  - e9f8633db0a2
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
 - name: fastq_manipulation
   owner: devteam
   revisions:
   - 5b87038565bb
+  - e30352e889fe
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
 - name: fasta_compute_length
   owner: devteam
   revisions:
+  - 5cbde03c1103
   - 7d37cfda8e00
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
 - name: fastq_paired_end_deinterlacer
   owner: devteam
   revisions:
+  - 523c2aff0376
   - f3936d0632cb
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
 - name: fastq_paired_end_interlacer
   owner: devteam
   revisions:
   - 2ccb8dcabddc
+  - b41c2c1bcfbf
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
 - name: flash
@@ -67,6 +73,7 @@ tools:
 - name: umi_tools_count
   owner: iuc
   revisions:
+  - 71ad4a56c40c
   - 8250ea3a1501
   - a535cf1e5da4
   - b557acca0b56
@@ -76,6 +83,7 @@ tools:
   owner: iuc
   revisions:
   - 6a675c3aa610
+  - 7a7e33d28f62
   - 99aea37a7ff7
   - f3759eec3018
   tool_panel_section_id: fasta_fastq
@@ -84,6 +92,7 @@ tools:
   owner: peterjc
   revisions:
   - 141612f8c3e3
+  - 85ef5f5a0562
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
 - name: length_and_gc_content

cloud/fastq_quality_control.yml.lock

@@ -21,6 +21,7 @@ tools:
   - 65b93b623c77
   - d60c3f704da0
   - dbf9c561ef29
+  - dbfc505896e9
   tool_panel_section_id: fastq_quality_control
   tool_panel_section_label: FASTQ Quality Control
 - name: fastqc
@@ -35,6 +36,7 @@ tools:
 - name: trimmomatic
   owner: pjbriggs
   revisions:
+  - b9aaed85cbd1
   - d94aff5ee623
   tool_panel_section_id: fastq_quality_control
   tool_panel_section_label: FASTQ Quality Control

cloud/graph_display_data.yml.lock

@@ -13,8 +13,8 @@ tools:
 - name: circos
   owner: iuc
   revisions:
-  - df7356989ac1
   - c4bde687c846
+  - df7356989ac1
   tool_panel_section_id: graph_display_data
   tool_panel_section_label: Graph/Display Data
 - name: jbrowse
@@ -27,9 +27,9 @@ tools:
 - name: volcanoplot
   owner: iuc
   revisions:
-  - 83c573f2e73c
-  - 73b8cb5bddcd
   - 2f557f6abbfb
+  - 73b8cb5bddcd
+  - 83c573f2e73c
   tool_panel_section_id: graph_display_data
   tool_panel_section_label: Graph/Display Data
 - name: pathview
@@ -42,9 +42,10 @@ tools:
 - name: ggplot2_heatmap2
   owner: iuc
   revisions:
-  - 53460afd5115
-  - 566197475670
-  - 4955e9bb96d1
   - 374e9062d874
+  - 4955e9bb96d1
+  - 51c6ccaace7e
+  - 53460afd5115
+  - '566197475670'
   tool_panel_section_id: graph_display_data
   tool_panel_section_label: Graph/Display Data

cloud/nanopore.yml.lock

@@ -13,6 +13,7 @@ tools:
 - name: flye
   owner: bgruening
   revisions:
+  - 1f0769f0b56b
   - 3e4f8642c77e
   - 3ee0ef312022
   tool_panel_section_id: nanopore
@@ -49,12 +50,14 @@ tools:
   owner: iuc
   revisions:
   - 28d7819c312f
+  - daf8518d243a
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
 - name: poretools_hist
   owner: iuc
   revisions:
   - 5a82eb9e1b89
+  - d1805f9c4c82
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
 - name: poretools_occupancy
@@ -67,17 +70,20 @@ tools:
   owner: iuc
   revisions:
   - 4fe6b96aff72
+  - 626b6c2be5c2
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
 - name: poretools_squiggle
   owner: iuc
   revisions:
+  - 26e6c9362b7b
   - 34553d0caa5e
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
 - name: poretools_yield_plot
   owner: iuc
   revisions:
+  - c5c5a3e84989
   - ca22d8497db5
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
@@ -91,42 +97,49 @@ tools:
 - name: poretools_winner
   owner: iuc
   revisions:
+  - 6d93709247c7
   - 79c1ac92f31b
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
 - name: poretools_times
   owner: iuc
   revisions:
+  - '107124859931'
   - 960be5e0b47e
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
 - name: poretools_tabular
   owner: iuc
   revisions:
   - 2cb2feb94f0e
+  - 5f5f1da94d7f
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
 - name: poretools_stats
   owner: iuc
   revisions:
   - 4b17acf9b6ab
+  - c1cbe2575d32
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
 - name: poretools_qualdist
   owner: iuc
   revisions:
+  - 72dfdbfab3cc
   - ae9060e764b5
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
 - name: poretools_nucdist
   owner: iuc
   revisions:
+  - 5c4fa65f5733
   - a57b6350fd5d
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
 - name: poretools_extract
   owner: iuc
   revisions:
+  - 08064da7b7fb
   - 7e4f1ed70187
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore

cloud/qiime2.yml.lock

@@ -6,6 +6,7 @@ tools:
 - name: suite_qiime2_core
   owner: q2d2
   revisions:
+  - 1dfccc639d50
   - 3f011fac899d
   tool_panel_section_id: qiime2
   tool_panel_section_label: QIIME2

cloud/rna_seq.yml

@@ -32,3 +32,7 @@ tools:
   owner: iuc
 - name: brew3r_r
   owner: iuc
+- name: seurat
+  owner: iuc
+- name: dexseq
+  owner: iuc

cloud/rna_seq.yml.lock

@@ -74,6 +74,7 @@ tools:
   owner: iuc
   revisions:
   - 1759d845181e
+  - 1b851f87fbe0
   - 38b6d12edc68
   - f3a5f075498f
   - f9d49f5cb597
@@ -82,6 +83,7 @@ tools:
 - name: cufflinks
   owner: devteam
   revisions:
+  - 6926716bbfb5
   - d080005cffe1
   tool_panel_section_id: rna_seq
   tool_panel_section_label: RNA-seq
@@ -114,5 +116,18 @@ tools:
   owner: iuc
   revisions:
   - 05f8e9d1e8b8
+  - d3b0390f325f
+  tool_panel_section_id: rna_seq
+  tool_panel_section_label: RNA-seq
+- name: seurat
+  owner: iuc
+  revisions:
+  - fab6ff46e019
+  tool_panel_section_id: rna_seq
+  tool_panel_section_label: RNA-seq
+- name: dexseq
+  owner: iuc
+  revisions:
+  - 9a7c5b6d8f1e
   tool_panel_section_id: rna_seq
   tool_panel_section_label: RNA-seq

cloud/rseqc.yml.lock

@@ -7,6 +7,7 @@ tools:
   owner: nilesh
   revisions:
   - 1a052c827e88
+  - 27e16a30667a
   - dbedfc5f5a3c
   tool_panel_section_id: rseqc
   tool_panel_section_label: RSeQC