HMSclient_CLI_install.md
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-
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-## All users should now use the [BioGrids Installer](client_install).
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-The HMS branded BioGrids Installer client is no longer developed and supported.
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-
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-This page is for archive purposes only.
HMSclient_install.md
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-
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-
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-## All users should now use the [BioGrids Installer](client_install).
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-The HMS branded BioGrids Installer client is no longer developed and supported.
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-
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-This page is for archive purposes only.
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-
client_CLI_install.md
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3 3
This page is for the BioGrids CLI (command line interface) software installation client for computers running Linux (CentOS/RHEL 7 recommended) or Apple OSX computers running MacOSX v10.10 - 10.14.
4 4
5
-Looking to get started with the BioGrids installation client? First, set up an account by registering here : [BioGrids registration](https://biogrids.org/registration/register/)
6 5
7
-A GUI version is also available for MacOS / OSX - [installation instructions can be found here](client_install).
8
-[GUI usage info is here](client_usage).
6
+
7
+- BioGrids Installation Manager - Downloads
8
+ - [Requirements](https://biogrids.org/wiki/client_downloads#requirements)
9
+ - [BioGrids nstallation Manager for MacOS and Linux, v2.4.0](https://biogrids.org/wiki/client_downloads#biogrids-installation-manager-for-macos-and-linux-v240)
10
+ - [BioGrids Command-line Installation Manager for MacOS and Linux, v2.4.0](https://biogrids.org/wiki/client_downloads#biogrids-command-line-installation-manager-for-macos-and-linux-v240)
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+
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+
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+
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+
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+
16
+Step 1 : [BioGrids registration](https://biogrids.org/registration/register/)
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+
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+
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10 20
### Pre-installation requirements
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downloads/ec2-ips.txt
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-
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-ec2-54-89-230-13.compute-1.amazonaws.com
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-
7
-ec2-54-174-30-59.compute-1.amazonaws.com
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-ec2-54-89-82-88.compute-1.amazonaws.com
12
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-
15
-ec2-3-92-229-216.compute-1.amazonaws.com
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-ec2-54-174-162-88.compute-1.amazonaws.com
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-ec2-3-91-218-4.compute-1.amazonaws.com
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-
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-ec2-54-197-13-190.compute-1.amazonaws.com
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-
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31
-ec2-34-239-117-183.compute-1.amazonaws.com
32
-
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-ec2-54-211-217-228.compute-1.amazonaws.com
36
-
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38
-
39
-ec2-18-233-9-76.compute-1.amazonaws.com
40
-
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-
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-
43
-ec2-3-85-32-62.compute-1.amazonaws.com
44
-
45
-
46
-
47
-ec2-3-83-179-145.compute-1.amazonaws.com
48
-
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-ec2-3-93-213-73.compute-1.amazonaws.com
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-
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-
54
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-ec2-184-72-159-181.compute-1.amazonaws.com
56
-
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59
-ec2-18-205-150-243.compute-1.amazonaws.com
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-
61
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63
-ec2-52-71-0-71.compute-1.amazonaws.com
64
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-ec2-34-201-34-106.compute-1.amazonaws.com
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71
-ec2-54-165-209-113.compute-1.amazonaws.com
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-ec2-54-204-78-139.compute-1.amazonaws.com
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79
-ec2-3-84-145-231.compute-1.amazonaws.com
80
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81
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82
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83
-ec2-54-91-133-5.compute-1.amazonaws.com
84
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86
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-ec2-3-95-154-132.compute-1.amazonaws.com
88
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90
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91
-ec2-3-84-101-187.compute-1.amazonaws.com
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-
r_packages.md
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2 2
3 3
Individual R packages are not listed in the [BioGrids Supported Applications](https://biogrids.org/software/) software list as they are too numerous.
4 4
5
-R packages for the current default version and the latest version of R are detailed in the table below.
5
+The quickest way to check availability of a package is to load the library in R.
6 6
7 7
If you would like to use a package that is not currently available through BioGrids send a request to: help@biogrids.org.
8 8
9
-A complete install of all Bioconductor packages is also available for site-wide installations.
10 9
11
-
12
-
13
-
14
-|Package|R 3.3.2 |R 3.5.1
15
-|---|---|---|
16
-|acepack|1.4.1|1.4.1|
17
-|ade4|1.7-10|1.7-13|
18
-|AnnotationDbi|1.36.2|1.44.0|
19
-|AnnotationHub|2.6.5|2.14.5|
20
-|askpass|1.1|1.1|
21
-|assertthat|0.2.1|0.2.1|
22
-|backports|1.1.2|1.1.4|
23
-|base|3.3.2|3.5.1|
24
-|base64enc|0.1-3|0.1-3|
25
-|BH|1.69.0-1|1.69.0-1|
26
-|Biobase|2.34.0|2.42.0|
27
-|BiocGenerics|0.20.0|0.28.0|
28
-|BiocParallel|1.8.2|1.16.6|
29
-|biomaRt|2.30.0|2.38.0|
30
-|Biostrings|2.42.1|2.50.2|
31
-|bit|1.1-12|1.1-14|
32
-|bit64|0.9-7|0.9-7|
33
-|bitops|1.0-6|1.0-6|
34
-|blob|1.1.0|1.1.1|
35
-|boot|1.3-20|1.3-20|
36
-|caTools|1.17.1|1.17.1.2|
37
-|checkmate|1.8.5|1.9.1|
38
-|class|7.3-14|7.3-15|
39
-|cli|1.0.0|1.1.0|
40
-|cluster|2.0.6|2.0.8|
41
-|codetools|0.2-15|0.2-16|
42
-|colorspace|1.3-2|1.4-1|
43
-|compiler|3.3.2|3.5.1|
44
-|crayon|1.3.4|1.3.4|
45
-|curl|3.3|3.3|
46
-|datasets|3.3.2|3.5.1|
47
-|data.table|1.10.4-3|1.12.2|
48
-|DBI|0.8|1.0.0|
49
-|digest|0.6.15|0.6.18|
50
-|dplyr|0.8.1|0.8.0.1|
51
-|ensembldb|1.6.2|2.6.8|
52
-|evaluate|0.10.1|0.13|
53
-|fansi|0.4.0|0.4.0|
54
-|foreign|0.8-69|0.8-71|
55
-|Formula|1.2-2|1.2-3|
56
-|futile.logger|1.4.3|1.4.3|
57
-|futile.options|1.0.0|1.0.1|
58
-|gdata|2.18.0|2.18.0|
59
-|GenomeInfoDb|1.10.3|1.18.2|
60
-|GenomicAlignments|1.10.1|1.18.1|
61
-|GenomicFeatures|1.26.4|1.34.8|
62
-|GenomicRanges|1.26.4|1.34.0|
63
-|ggplot2|2.2.1|3.1.1|
64
-|glue|1.3.1|1.3.1|
65
-|gplots|3.0.1|3.0.1.1|
66
-|graphics|3.3.2|3.5.1|
67
-|grDevices|3.3.2|3.5.1|
68
-|grid|3.3.2|3.5.1|
69
-|gridExtra|2.3|2.3|
70
-|gtable|0.2.0|0.3.0|
71
-|gtools|3.5.0|3.8.1|
72
-|highr|0.6|0.8|
73
-|Hmisc|4.1-1|4.2-0|
74
-|htmlTable|1.11.2|1.13.1|
75
-|htmltools|0.3.6|0.3.6|
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-|htmlwidgets|1.0|1.3|
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-|httpuv|1.5.1|1.5.1|
78
-|httr|1.4.0|1.4.0|
79
-|igraph|1.2.4.1|1.2.4|
80
-|interactiveDisplayBase|1.12.0|1.20.0|
81
-|IRanges|2.8.2|2.16.0|
82
-|jsonlite|1.5|1.6|
83
-|KernSmooth|2.23-15|2.23-15|
84
-|knitr|1.20|1.22|
85
-|labeling|0.3|0.3|
86
-|lambda.r|1.2|1.2.3|
87
-|later|0.8.0|0.8.0|
88
-|lattice|0.20-35|0.20-38|
89
-|latticeExtra|0.6-28|0.6-28|
90
-|lazyeval|0.2.1|0.2.2|
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-|magrittr|1.5|1.5|
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-|markdown|0.8|0.9|
93
-|MASS|7.3-49|7.3-51.3|
94
-|Matrix|1.2-12|1.2-17|
95
-|memoise|1.1.0|1.1.0|
96
-|methods|3.3.2|3.5.1|
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-|mgcv|1.8-23|1.8-28|
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-|mime|0.5|0.6|
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-|munsell|0.4.3|0.5.0|
100
-|mvtnorm|1.0-7|1.0-10|
101
-|nlme|3.1-131.1|3.1-139|
102
-|nnet|7.3-12|7.3-12|
103
-|openssl|1.4|1.3|
104
-|Package|Version|Version|
105
-|parallel|3.3.2|3.5.1|
106
-|pheatmap|1.0.12|1.0.12|
107
-|pillar|1.4.1|1.3.1|
108
-|pkgconfig|2.0.2|2.0.2|
109
-|plogr|0.2.0|0.2.0|
110
-|plyr|1.8.4|1.8.4|
111
-|png|0.1-7|0.1-7|
112
-|promises|1.0.1|1.0.1|
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-|purrr|0.3.2|0.3.2|
114
-|R6|2.4.0|2.4.0|
115
-|RColorBrewer|1.1-2|1.1-2|
116
-|Rcpp|1.0.1|1.0.1|
117
-|RCurl|1.95-4.10|1.95-4.12|
118
-|reshape2|1.4.3|1.4.3|
119
-|rlang|0.3.4|0.3.4|
120
-|rpart|4.1-13|4.1-15|
121
-|Rsamtools|1.26.2|1.34.1|
122
-|RSQLite|2.0|2.1.1|
123
-|rstudioapi|0.7|0.10|
124
-|rtracklayer|1.34.2|1.42.2|
125
-|S4Vectors|0.12.2|0.20.1|
126
-|scales|0.5.0|1.0.0|
127
-|shiny|1.3.2|1.3.1|
128
-|snow|0.4-2|0.4-3|
129
-|sourcetools|0.1.7|0.1.7|
130
-|spatial|7.3-11|7.3-11|
131
-|splines|3.3.2|3.5.1|
132
-|stats|3.3.2|3.5.1|
133
-|stats4|3.3.2|3.5.1|
134
-|stringi|1.1.7|1.4.3|
135
-|stringr|1.3.0|1.4.0|
136
-|SummarizedExperiment|1.4.0|1.12.0|
137
-|survival|2.41-3|2.44-1.1|
138
-|sys|3.2|3.1|
139
-|tcltk|3.3.2|3.5.1|
140
-|tibble|2.1.3|2.1.1|
141
-|tidyr|0.8.3|0.8.3|
142
-|tidyselect|0.2.5|0.2.5|
143
-|tools|3.3.2|3.5.1|
144
-|utf8|1.1.3|1.1.4|
145
-|utils|3.3.2|3.5.1|
146
-|viridis|0.5.0|0.5.1|
147
-|viridisLite|0.3.0|0.3.0|
148
-|withr|2.1.1|2.1.2|
149
-|xtable|1.8-2|1.8-3|
150
-|XVector|0.14.1|0.22.0|
151
-|yaml|2.1.18|2.2.0|
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-|zlibbioc|1.20.0|1.28.0|
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-|zoo|1.8-1|1.8-5|
recommended.md
... ...
@@ -1,7 +1,8 @@
1 1
# Recommended Hardware
2 2
3 3
## Linux Workstations
4
-BioGrids's preferred hardware vendor is [ThinkMate](http://thinkmate.com) and we have some [recommended configurations](http://www.thinkmate.com/sbgrid) for structural biology computing. Please feel free to contact us at help@sbgrid.org regarding upcoming hardware purchases if you have questions - we'd be happy to advise.
4
+BioGrids's preferred hardware vendor is [ThinkMate](http://thinkmate.com) and we have some [recommended configurations](http://www.thinkmate.com/sbgrid). Please feel free to contact us at help@biogrids.org regarding upcoming hardware purchases if you have questions - we'd be happy to advise.
5 5
6 6
## Apple Workstations
7
-Any Apple machine can be a capable computer for structural biology. The basic Apple educational discount is available through their online web store, and your institution may have negotiated an even better deal with their Apple representative. BioGrids has several labs that run exclusively on Macs and OS X.
7
+Any Apple machine with OSX 10.14 or later will run BioGrids software. BioGrids has several labs that run exclusively on Macs and OS X.
8
+
versions.md
... ...
@@ -4,49 +4,58 @@ Most of the software titles installed in the BioGrids software collection have s
4 4
5 5
## Display Available Versions
6 6
7
-To list the available versions of a software title, you can use the *biogrids* utility. Running *biogrids -l* will list the versions for your current platform. From a Linux machine, a search for samtools versions looks like this:
8
-
9
- $ ./biogrids -l samtools
10
- 0.1.19
11
- 1.3
12
- 1.3.1
13
- 1.4.1
14
- 1.5 (default)
15
-
16
-
17
-Running *biogrids -L* will print the available versions for the current platforms, OS X and Linux.
18
-
19
-
20
- $ ./biogrids -L samtools
21
- i386-mac:
22
- -0.1.19
23
- -1.3
24
- -1.3.1
25
- -1.4.1
26
- -1.5 (default)
27
- x86_64-linux:
28
- -0.1.19
29
- -1.3
30
- -1.3.1
31
- -1.4.1
32
- -1.5 (default)
7
+To list the available versions of a software title, you can use the *biogrids-info* utility. Running *biogrids-info -l* will list the versions for your current platform. From a Linux machine, a search for samtools versions looks like this:
8
+
9
+ $ biogrids-info -l samtools
10
+ Version information for: /programs/x86_64-linux/samtools
11
+
12
+ Default version: 1.13
13
+ In-use version: 1.13
14
+
15
+ Installed versions: 1.13 1.12 1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19
16
+ Other available versions: 1.12 1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19
17
+ Overrides use this shell variable: SAMTOOLS_X
18
+
19
+
20
+Running *biogrids-info -L* will print the available versions for the current platforms, OS X and Linux.
21
+
22
+
23
+ $ biogrids-info -L samtools
24
+ Version information for: /programs/x86_64-linux/samtools
25
+
26
+ Default version: 1.13
27
+ In-use version: 1.13
28
+
29
+ Installed versions: 1.13 1.12 1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19
30
+ Other available versions: 1.12 1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19
31
+ Overrides use this shell variable: SAMTOOLS_X
32
+
33
+ No program directory by that name found in /programs/i386-linux.
34
+ Version information for: /programs/i386-mac/samtools
35
+
36
+ Default version: 1.13
37
+
38
+ Installed versions: 1.13 1.12 1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19 1.13 1.12 1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19
39
+ Other available versions: 1.12 1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19
40
+ Overrides use this shell variable: SAMTOOLS_X
41
+
42
+ No program directory by that name found in /programs/powermac.
33 43
34 44
35 45
## Overriding Default Versions
36 46
37 47
To override the default version of a software title, you need to create an override file. The shell configuration scripts will read this file and override the default version.
38 48
39
-The override file is named .sbgrid.conf and should be placed in your $HOME directory. The syntax for overrides is a simple key=value pair. E.g. it should look like this:
49
+The override file is named .sbgrid.conf (begins with a dot) and should be placed in your $HOME directory. The syntax for overrides is a simple key=value pair. E.g. it should look like this:
40 50
41 51
`APPLICATION_X=1.2`
42 52
43 53
APPLICATION_X is the name of the application followed by an underscore and the shorthand initial for the architecture. The last field on the line is the software version number you want to use. The initials for each software branch are:
44 54
45
-| Software Directory | Shorthand Initial |
46
-| ------------------ | ----------------- |
47
-| i386-linux | _L |
48
-| x86_64-linux | _X |
49
-| i386-mac | _M |
55
+| Architecture | Shorthand Initial |
56
+| ------------ | ----------------- |
57
+| Linux | _X |
58
+| Mac | _M |
50 59
51 60
To quickly open the overrides file in your default $EDITOR, you can run *sbgrid-overrides -e*.
52 61