| ... |
... |
@@ -1,6 +1,6 @@ |
| 1 |
1 |
## BioGrids installation client CLI |
| 2 |
2 |
|
| 3 |
|
-This page is for the BioGrids CLI (command line interface) software installation client for computers running Linux (CentOS/RHEL 6 or 7 recommended) or Apple OSX computers running MacOSX v10.10 - 10.13. |
| |
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 |
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 |
6 |
|
| ... |
... |
@@ -21,9 +21,7 @@ A GUI version is also available for MacOS / OSX - [installation instructions can |
| 21 |
21 |
**For large packages (R, Bioconductor), a wired connection is recommended.** |
| 22 |
22 |
Some packages are quite large and can be slow to download, especially over WiFi. |
| 23 |
23 |
|
| 24 |
|
-**pip** |
| 25 |
|
- pip is a package management system used to install and manage software packages written in Python. The software installation client is installable by pip. This may not be on you machine by default, instructions for adding it are included here. |
| 26 |
|
- ### Binary releases : MacOS and Linux Installation |
| |
24 |
+### Binary releases : MacOS and Linux Installation |
| 27 |
25 |
|
| 28 |
26 |
There is minimal installation needed for these binaries. They can be run from any location. Untar the archive, make the file executable if necessary, and run from your preferred location. |
| 29 |
27 |
|
| ... |
... |
@@ -58,69 +56,8 @@ A GUI version is also available for MacOS / OSX - [installation instructions can |
| 58 |
56 |
biogrids: error: too few arguments |
| 59 |
57 |
``` |
| 60 |
58 |
|
| 61 |
|
-### pip - Mac Installation |
| 62 |
59 |
|
| 63 |
|
- On mac, pip is available from [macports](https://www.macports.org/), [homebrew](http://brew.sh/), and [fink](http://finkproject.org/). It also can be added using **easy_install**. easy_install will install pip into your system python. |
| 64 |
|
- |
| 65 |
|
- $ sudo easy_install pip |
| 66 |
|
- |
| 67 |
|
-###pip - Linux Installation |
| 68 |
|
- |
| 69 |
|
- On CentOS6, you can install pip from the EPEL repository (yum -y install python-pip) or as [per these directions](https://pip.pypa.io/en/stable/installing/) |
| 70 |
|
- |
| 71 |
|
-## CLI client - Installation and activation |
| 72 |
|
-**1. Download the latest BioGrids installation client from here.** |
| 73 |
|
- |
| 74 |
|
-[Latest build : 1.0.694, 2018-03-22](downloads/biogrids-1.0.694-py2-none-any.whl) |
| 75 |
|
- |
| 76 |
|
-**2. Install / Upgrade with pip** |
| 77 |
|
- |
| 78 |
|
- $ sudo pip install biogrids-1.0.694-py2-none-any.whl |
| 79 |
|
- |
| 80 |
|
- Which should produce output similar to : |
| 81 |
|
- |
| 82 |
|
-``` |
| 83 |
|
-Unpacking ./biogrids-1.0.694-py2-none-any.whl |
| 84 |
|
-Requirement already satisfied (use --upgrade to upgrade): pyasn1 in /nfs/programs-dev/i386-mac/python/2.7.5/lib/python2.7/site-packages (from BioGrids-Installer==1.0.488) |
| 85 |
|
-Downloading/unpacking requests (from BioGrids-Installer==1.0b2.dev412) |
| 86 |
|
- Downloading requests-2.11.1.tar.gz (485kB): 485kB downloaded |
| 87 |
|
- Running setup.py egg_info for package requests |
| 88 |
|
- |
| 89 |
|
- warning: no files found matching 'test_requests.py' |
| 90 |
|
-Installing collected packages: BioGrids-Installer, requests |
| 91 |
|
- Running setup.py install for requests |
| 92 |
|
- |
| 93 |
|
- warning: no files found matching 'test_requests.py' |
| 94 |
|
-Successfully installed BioGrids-Installer requests |
| 95 |
|
-Cleaning up... |
| 96 |
|
-``` |
| 97 |
|
- |
| 98 |
|
-The *biogrids* command will produce this usage info : |
| 99 |
|
- |
| 100 |
|
- $ biogrids |
| 101 |
|
- |
| 102 |
|
-``` |
| 103 |
|
-usage: |
| 104 |
|
-biogrids <command> [<command_args>] |
| 105 |
|
- |
| 106 |
|
-Available commands are: |
| 107 |
|
- activate Activate new installation |
| 108 |
|
- list List available packages |
| 109 |
|
- info Print package metadata |
| 110 |
|
- install Install single package |
| 111 |
|
- install-all Install all packages from collection |
| 112 |
|
- installed List installed packages |
| 113 |
|
- remove Remove installed package |
| 114 |
|
- resume Resume interrupted installations |
| 115 |
|
- upgrades List available upgrades for installed packages |
| 116 |
|
- upgrade Upgrade package to latest version |
| 117 |
|
- upgrade-all Upgrade all packages to latest version |
| 118 |
|
- version Print package version string |
| 119 |
|
-biogrids: error: too few arguments |
| 120 |
|
- |
| 121 |
|
-``` |
| 122 |
|
- |
| 123 |
|
-**4. Activate the installation** |
| |
60 |
+** Activate the installation** |
| 124 |
61 |
Enter your site and key which you should have received these by email. |
| 125 |
62 |
|
| 126 |
63 |
$ biogrids activate <site name> <user name> <activation key> |
