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sbgrid-cli-admin.md
... | ... | @@ -2,7 +2,22 @@ |
2 | 2 | |
3 | 3 | One of the primary benefits of an SBGrid software installation is that it is a managed software stack. New titles are added, obsolete versions are removed, and updates happen automatically. |
4 | 4 | New software and bug fixes are an email away (bugs@sbgrid.org) without requiring local administrators or system admistration expertise. While there are other modes available (GUI, granular versions, titles, etc), this is the recommended mode of installation for most sites. |
5 | - |
|
5 | +### Pre-Installation |
|
6 | + |
|
7 | +| Installation Requirements | | |
|
8 | +| ------------------------- | --------------------------------------------------- | |
|
9 | +| Hard Drive Space | ~1 Tb recommended for full installation | |
|
10 | +| Operating System | Linux, macOS | |
|
11 | +| Privileges | sudo root or administrator account (macOS) | |
|
12 | +| network | Outbound https, rsync |
|
13 | + |
|
14 | +**Approximate size per Branch** |
|
15 | + |
|
16 | +| Branch | size | |
|
17 | +| ------------ | ------ | |
|
18 | +| i386-mac | ~400 Gb | |
|
19 | +| x86_64-linux | ~600 Gb | |
|
20 | +| shared files | ~40 Gb | |
|
6 | 21 | ### SBGrid installation manager admin mode |
7 | 22 | |
8 | 23 | sbgrid-cli admin mode replaces the sbgrid-admin script installation method used previously to install and automatically update SBGrid installations. `sbgrid-cli admin` offers a some advantages: |
... | ... | @@ -20,7 +35,7 @@ An SBGrid installation manager account is required. [Please register here for an |
20 | 35 | Accounts are available for lab members and IT support staff. |
21 | 36 | ## Installation Steps: |
22 | 37 | |
23 | -1. Create an 'sbgrid' user on the machine that will host your software installation. |
|
38 | +**1. Create an 'sbgrid' user** on the machine that will host your software installation. |
|
24 | 39 | This step is not strictly required, but is highly recommended. |
25 | 40 | |
26 | 41 | ``` |
... | ... | @@ -37,13 +52,13 @@ echo 'sbgrid ALL=(ALL) ALL' > /etc/sudoers.d/sbgrid |
37 | 52 | |
38 | 53 | This is only required for the activation step. '/etc/sudoers.d/sbgrid' can be removed anytime after the installation is activated. |
39 | 54 | |
40 | -2. Log in as this 'sbgrid' user |
|
55 | +**2. Log in as this 'sbgrid' user** |
|
41 | 56 | |
42 | 57 | ``` |
43 | 58 | su sbgrid |
44 | 59 | ``` |
45 | 60 | |
46 | -3. Download the sbgrid-cli application here: |
|
61 | +**3. Download the sbgrid-cli application** |
|
47 | 62 | [https://sbgrid.org/wiki/client_downloads](client_downloads) |
48 | 63 | |
49 | 64 | For Linux: |
... | ... | @@ -55,13 +70,13 @@ For Mac: |
55 | 70 | curl -LO https://sbgrid-installation-manager.s3.amazonaws.com/2.4.0/sbgrid-cli_2.4.0-macos.tar.gz |
56 | 71 | ``` |
57 | 72 | |
58 | -4. Untar the archive and make it executable by running 'chmod +x sbgrid-cli' |
|
73 | +**4. Untar the archive and make it executable** by running 'chmod +x sbgrid-cli' |
|
59 | 74 | |
60 | 75 | ``` |
61 | 76 | tar -zxvf sbgrid-cli_2.4.0-linux.tar.gz && chmod +x sbgrid-cli |
62 | 77 | ``` |
63 | 78 | |
64 | -5. Activate the installation |
|
79 | +**5. Activate the installation** |
|
65 | 80 | |
66 | 81 | Activating the installation will create the required installation paths and directories for installing the software. This is the point where alternate installation paths can be used. Please see [https://sbgrid.org//wiki/sbgrid-cli#activation](https://sbgrid.org//wiki/sbgrid-cli#activation) for more info. |
67 | 82 | |
... | ... | @@ -77,12 +92,12 @@ If the sbgrid user does not have sudo access, use |
77 | 92 | ``` |
78 | 93 | where the target path is writable. This option does not require sudo but will require manual creation of the /programs symlink to the target installation directory. This is not required for installation and updates, only for using the software. It may not be needed on servers that host the programs as a network share. |
79 | 94 | |
80 | -6. Run the installation using `./sbgrid-cli admin` |
|
95 | +**6. Run the installation** using `./sbgrid-cli admin` |
|
81 | 96 | |
82 | -7. Add to crontab for periodic updates using `./sbgrid-cli crontab` |
|
97 | +**7. Add to crontab** for periodic updates using `./sbgrid-cli crontab` |
|
83 | 98 | |
84 | 99 | |
85 | -Post-Install Steps: |
|
100 | +### Post-Install Steps: |
|
86 | 101 | |
87 | 102 | 1. Once the download has completed, you'll need to add a symlink in |
88 | 103 | the root directory of each machine that wants to use the software. |
... | ... | @@ -119,6 +134,11 @@ To make this automatic, add a crontab entry. This can be done from `sbgrid-cli` |
119 | 134 | sbgrid-cli crontab |
120 | 135 | ``` |
121 | 136 | |
137 | +Admin mode - all versions, all titles mac and linux, 4 processes |
|
138 | +``` |
|
139 | +sbgrid-cli crontab --all-versions --darwin --linux -j 4 |
|
140 | +``` |
|
141 | + |
|
122 | 142 | For more info on cron, see [https://www.man7.org/linux/man-pages/man5/crontab.5.html](https://www.man7.org/linux/man-pages/man5/crontab.5.html) |
123 | 143 | |
124 | 144 | ## Migrating existing site installations |