Downloads:

1,504

Downloads of v 1.14:

582

Last Update:

06 Dec 2019

Package Maintainer(s):

Software Author(s):

  • UCSF Resource for Biocomputing
  • Visualization
  • and Informatics

Tags:

chimera chemistry molecular modeling python nonsilent admin

UCSF Chimera

1.14 | Updated: 06 Dec 2019

Downloads:

1,504

Downloads of v 1.14:

582

Maintainer(s):

Software Author(s):

  • UCSF Resource for Biocomputing
  • Visualization
  • and Informatics

UCSF Chimera 1.14

All Checks are Passing

2 Passing Test


Validation Testing Passed


Verification Testing Passed

Details

To install UCSF Chimera, run the following command from the command line or from PowerShell:

>

To upgrade UCSF Chimera, run the following command from the command line or from PowerShell:

>

To uninstall UCSF Chimera, run the following command from the command line or from PowerShell:

>

NOTE: This applies to both open source and commercial editions of Chocolatey.

1. Ensure you are set for organizational deployment

Please see the organizational deployment guide

  • Open Source or Commercial:
    • Proxy Repository - Create a proxy nuget repository on Nexus, Artifactory Pro, or a proxy Chocolatey repository on ProGet. Point your upstream to https://chocolatey.org/api/v2. Packages cache on first access automatically. Make sure your choco clients are using your proxy repository as a source and NOT the default community repository. See source command for more information.
    • You can also just download the package and push it to a repository Download

3. Enter your internal repository url

(this should look similar to https://chocolatey.org/api/v2)

4. Choose your deployment method:


choco upgrade chimera -y --source="'STEP 3 URL'" [other options]

See options you can pass to upgrade.

See best practices for scripting.

Add this to a PowerShell script or use a Batch script with tools and in places where you are calling directly to Chocolatey. If you are integrating, keep in mind enhanced exit codes.

If you do use a PowerShell script, use the following to ensure bad exit codes are shown as failures:


choco upgrade chimera -y --source="'STEP 3 URL'"
$exitCode = $LASTEXITCODE

Write-Verbose "Exit code was $exitCode"
$validExitCodes = @(0, 1605, 1614, 1641, 3010)
if ($validExitCodes -contains $exitCode) {
  Exit 0
}

Exit $exitCode

- name: Ensure chimera installed
  win_chocolatey:
    name: chimera
    state: present
    version: 1.14
    source: STEP 3 URL

See docs at https://docs.ansible.com/ansible/latest/modules/win_chocolatey_module.html.

Coming early 2020! Central Managment Reporting available now! More information...


chocolatey_package 'chimera' do
  action    :install
  version  '1.14'
  source   'STEP 3 URL'
end

See docs at https://docs.chef.io/resource_chocolatey_package.html.


Chocolatey::Ensure-Package
(
    Name: chimera,
    Version: 1.14,
    Source: STEP 3 URL
);

Requires Otter Chocolatey Extension. See docs at https://inedo.com/den/otter/chocolatey.


cChocoPackageInstaller chimera
{
   Name     = 'chimera'
   Ensure   = 'Present'
   Version  = '1.14'
   Source   = 'STEP 3 URL'
}

Requires cChoco DSC Resource. See docs at https://github.com/chocolatey/cChoco.


package { 'chimera':
  provider => 'chocolatey',
  ensure   => '1.14',
  source   => 'STEP 3 URL',
}

Requires Puppet Chocolatey Provider module. See docs at https://forge.puppet.com/puppetlabs/chocolatey.


salt '*' chocolatey.install chimera version="1.14" source="STEP 3 URL"

See docs at https://docs.saltstack.com/en/latest/ref/modules/all/salt.modules.chocolatey.html.

5. If applicable - Chocolatey configuration/installation

See infrastructure management matrix for Chocolatey configuration elements and examples.

Private CDN cached downloads available for licensed customers. Never experience 404 breakages again! Learn more...

This package was approved by moderator flcdrg on 08 Dec 2019.

Description

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, nonprofit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI), funded by the National Institutes of Health (NIGMS P41-GM103311).

Non-Commercial use ONLY

Use of the Chimera is restricted to non-commercial, personal, academic, non-profit, or government-sponsored research purposes. Commercial use of the Software requires a separately executed written license agreement.


tools\chocolateyinstall.ps1
$ErrorActionPreference = 'Stop'

$BaseURL = 'https://www.cgl.ucsf.edu'

# Discovering download link
# Process found here:  https://stackoverflow.com/questions/34422255/
# Unsure if all settings are needed.
$url = "$BaseURL/chimera/cgi-bin/secure/chimera-get.py"
$postData = "choice=Accept&file=win64/chimera-$env:ChocolateyPackageVersion-win64.exe"
$buffer = [text.encoding]::ascii.getbytes($postData)
[net.httpWebRequest] $req = [net.webRequest]::create($url)
$req.method = "POST"
$req.Accept = "text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8"
$req.Headers.Add("Accept-Language: en-US")
$req.Headers.Add("Accept-Encoding: gzip,deflate")
$req.Headers.Add("Accept-Charset: ISO-8859-1,utf-8;q=0.7,*;q=0.7")
$req.AllowAutoRedirect = $false
$req.ContentType = "application/x-www-form-urlencoded"
$req.ContentLength = $buffer.length
$req.TimeOut = 50000
$req.KeepAlive = $true
$req.Headers.Add("Keep-Alive: 300");
$reqst = $req.getRequestStream()
$reqst.write($buffer, 0, $buffer.length)
$reqst.flush()
$reqst.close()
[net.httpWebResponse] $res = $req.getResponse()
$resst = $res.getResponseStream()
$sr = new-object IO.StreamReader($resst)
$result = $sr.ReadToEnd()
$res.close()

$URLstub = ($result.split() |? {$_ -match 'href='}) -replace '.*href="(.*)".*','$1'

Write-Host 'You are establishing a license agreement as defined here:' -ForegroundColor Cyan
Write-Host 'http://www.cgl.ucsf.edu/chimera/license.html' -ForegroundColor Cyan

$packageArgs = @{
   packageName   = $env:ChocolateyPackageName
   fileType      = 'EXE'
   url64bit      = $BaseURL + $URLstub
   softwareName  = 'UCSF Chimera*' 
   checksum64    = '7607b11115ba8cbaa87e9f0c8362334b753b531e66dc1341a49dd24802934f80'
   checksumType64= 'sha256'
   silentArgs   = '/VERYSILENT /SUPPRESSMSGBOXES /NORESTART /SP-'
   validExitCodes= @(0)
}

Install-ChocolateyPackage @packageArgs

Log in or click on link to see number of positives.

In cases where actual malware is found, the packages are subject to removal. Software sometimes has false positives. Moderators do not necessarily validate the safety of the underlying software, only that a package retrieves software from the official distribution point and/or validate embedded software against official distribution point (where distribution rights allow redistribution).

Chocolatey Pro provides runtime protection from possible malware.

Version Downloads Last Updated Status
UCSF Chimera 1.13.1 548 Friday, November 30, 2018 Approved
UCSF Chimera 1.13 136 Friday, August 3, 2018 Approved
UCSF Chimera 1.12 238 Thursday, February 22, 2018 Approved

This package has no dependencies.

Discussion for the UCSF Chimera Package

Ground Rules:

  • This discussion is only about UCSF Chimera and the UCSF Chimera package. If you have feedback for Chocolatey, please contact the Google Group.
  • This discussion will carry over multiple versions. If you have a comment about a particular version, please note that in your comments.
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  • Tell us what you love about the package or UCSF Chimera, or tell us what needs improvement.
  • Share your experiences with the package, or extra configuration or gotchas that you've found.
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