-
Notifications
You must be signed in to change notification settings - Fork 35
/
rna_workbench_2.yml
174 lines (146 loc) · 5.45 KB
/
rna_workbench_2.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
---
# This is a sample file to be used as a reference for populating a list of
# tools that you wish to install into Galaxy from a Tool Shed via the
# `install_tool_shed_tools.py` script.
#
# For each tool you want to install, you must provide the following keys:
# * name: this is is the name of the tool to install
# * owner: owner of the Tool Shed repository from where the tools is being
# installed
# Further, you need to provide **one** of the following two keys:
# * tool_panel_section_id: ID of the tool panel section where you want the
# tool to be installed. The section ID can be found
# in Galaxy's `shed_tool_conf.xml` config file. Note
# that the specified section must exist in this file.
# Otherwise, the tool will be installed outside any
# section.
# * tool_panel_section_label: Display label of a tool panel section where
# you want the tool to be installed. If it does not
# exist, this section will be created on the target
# Galaxy instance (note that this is different than
# when using the ID).
# Multi-word labels need to be placed in quotes.
# Each label will have a corresponding ID created;
# the ID will be an all lowercase version of the
# label, with multiple words joined with
# underscores (e.g., 'BED tools' -> 'bed_tools').
#
# Tou can also specify the following optional keys to further define the
# installation properties:
# * tool_shed_url: the URL of the Tool Shed from where the tool should be
# installed. (default: https://toolshed.g2.bx.psu.edu)
# * revisions: a list of revisions of the tool, all of which will attempt to
# be installed. (default: latest)
# * install_tool_dependencies: True or False - whether to install tool
# dependencies or not. (default: True)
# * install_repository_dependencies: True or False - whether to install repo
# dependencies or not. (default: True)
api_key: admin
galaxy_instance: http://localhost:8080
install_tool_dependencies: false
tools:
# RNA-protein Interaction
- name: dorina
owner: rnateam
install_resolver_dependencies: true
tool_panel_section_label: "RNA-protein Interaction"
- name: piranha
owner: rnateam
install_resolver_dependencies: true
tool_panel_section_label: "RNA-protein Interaction"
- name: rnacommender
owner: rnateam
install_resolver_dependencies: false
tool_panel_section_label: "RNA-protein Interaction"
- name: intarna
owner: rnateam
install_resolver_dependencies: true
tool_panel_section_label: "RNA-RNA Interaction"
- name: paralyzer
owner: rnateam
install_resolver_dependencies: false
tool_panel_section_label: "RNA-protein Interaction"
install_resolver_dependencies: false
- name: aresite2
owner: rnateam
install_resolver_dependencies: true
tool_panel_section_label: "RNA-protein Interaction"
install_resolver_dependencies: false
# RNA Annotation
- name: gotohscan
owner: rnateam
install_resolver_dependencies: false
tool_panel_section_label: "RNA Annotation"
- name: rnacode
owner: rnateam
install_resolver_dependencies: false
tool_panel_section_label: "RNA Annotation"
- name: infernal
owner: bgruening
install_resolver_dependencies: true
tool_panel_section_label: "RNA Annotation"
tool_shed_url: https://toolshed.g2.bx.psu.edu
revisions:
- c47a7c52ac4f
- 6e18e0b098cd
- name: trna_prediction
owner: bgruening
install_resolver_dependencies: true
tool_panel_section_label: "RNA Annotation"
- name: rnabob
owner: rnateam
install_resolver_dependencies: false
tool_panel_section_label: "RNA Annotation"
- name: fuma
owner: yhoogstrate
install_resolver_dependencies: true
tool_panel_section_label: "RNA Annotation"
- name: rcas
owner: rnateam
install_resolver_dependencies: true
tool_panel_section_label: "RNA Annotation"
install_resolver_dependencies: false
# Ribosome Profiling
- name: ribotaper
owner: rnateam
install_resolver_dependencies: false
tool_panel_section_label: "Ribosome Profiling"
# RNA-Seq
- name: sortmerna
owner: rnateam
install_resolver_dependencies: true
tool_panel_section_label: "RNA-Seq"
- name: data_manager_sortmerna_database_downloader
install_resolver_dependencies: true
owner: rnateam
- name: blockclust
owner: rnateam
install_resolver_dependencies: true
tool_panel_section_label: "RNA-Seq"
- name: flaimapper
owner: yhoogstrate
install_resolver_dependencies: true
tool_panel_section_label: "RNA-Seq"
#- name: suite_mirdeep_2_0
# owner: rnateam
# tool_panel_section_label: "RNA-Seq"
# tool_shed_url: https://toolshed.g2.bx.psu.edu
# install_resolver_dependencies: True
# install_tool_dependencies: False
- name: pipmir
owner: rnateam
install_resolver_dependencies: false
tool_panel_section_label: "RNA-Seq"
- name: nastiseq
owner: rnateam
install_resolver_dependencies: false
tool_panel_section_label: "RNA-Seq"
# RNA Target Prediction
- name: targetfinder
owner: rnateam
install_resolver_dependencies: true
tool_panel_section_label: "RNA Target Prediction"
- name: mqc
owner: rnateam
install_resolver_dependencies: true
tool_panel_section_label: "Quality Control"