Downloads:

214

Downloads of v 2.6.6:

129

Last Update:

11/30/2018

Package Maintainer(s):

Software Author(s):

  • Technelysium

Tags:

chromas trace sequence DNA chromatogram biosystems embedded

Chromas

2.6.6 | Updated: 11/30/2018

Downloads:

214

Downloads of v 2.6.6:

129

Maintainer(s):

Software Author(s):

  • Technelysium

Chromas 2.6.6

All Checks are Passing

2 Passing Test


Validation Testing Passed


Verification Testing Passed

Details

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

>

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

>

To uninstall Chromas, 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 chromas -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 chromas -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 chromas installed
  win_chocolatey:
    name: chromas
    state: present
    version: 2.6.6
    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 'chromas' do
  action    :install
  version  '2.6.6'
  source   'STEP 3 URL'
end

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


Chocolatey::Ensure-Package
(
    Name: chromas,
    Version: 2.6.6,
    Source: STEP 3 URL
);

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


cChocoPackageInstaller chromas
{
   Name     = 'chromas'
   Ensure   = 'Present'
   Version  = '2.6.6'
   Source   = 'STEP 3 URL'
}

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


package { 'chromas':
  provider => 'chocolatey',
  ensure   => '2.6.6',
  source   => 'STEP 3 URL',
}

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


salt '*' chocolatey.install chromas version="2.6.6" 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.

This package was approved by moderator gep13 on 12/3/2018.

Description

Chromas is a free trace viewer for simple DNA sequencing projects which do not require assembly of multiple sequences.

Chromas

Features:

  • Opens .ab1 chromatogram files from Applied Biosystems DNA sequencers.
  • Opens SCF and ZTR format chromatogram files created by other sequencers or retrieved from databases.
  • Save in .scf or Applied Biosystems .ab1 format.
  • Print a chromatogram with options to zoom or fit to one page.
  • Automatic removal of low-quality sequence (when quality data is available) or vector sequences.
  • Export sequences in plain text, FASTA, FASTQ, EMBL, GenBank or GCG formats, or formatted with base numbering for presentation.
  • Copy the sequence to the clipboard in plain text, FASTA or FASTQ format for pasting into other applications.
  • Reverse and complement the sequence and chromatogram.
  • Search for subsequences by exact matching or optimal alignment.
  • Display translations in 3 frames along with the sequence.
  • Copy an image of a chromatogram section for pasting into documents or presentations.
  • Batch processing, including format conversion, sequence export with vector removal, batch printing and batch export of raw data.
  • Enhance .ab1 files using the PeakTrace RP component from Nucleics Pty Ltd to improve peak readability and extract more high-quality bases.

Chromas is free of charge. The PeakTrace RP component requires registration for a free account, and is a paid service after the 40 free units have been used. An introductory discount is available by following the link under the Options menu in Chromas.


tools\chocolateyinstall.ps1
$ErrorActionPreference = 'Stop'

$toolsDir   = Split-Path -parent $MyInvocation.MyCommand.Definition
$fileLocation = (Get-ChildItem -Path $toolsDir -Filter '*.exe').FullName

$InstallArgs = @{
   packageName    = $env:ChocolateyPackageName
   FileType       = 'exe'
   File           = $fileLocation
   silentArgs     = "/VERYSILENT /SUPPRESSMSGBOXES /NORESTART /SP-"
   validExitCodes = @(0)
}

Install-ChocolateyInstallPackage @InstallArgs
New-Item "$fileLocation.ignore" -Type file -Force | Out-Null
tools\Chromas266Setup.exe
md5: 3C4663B431305421BE750C4F6AF3A993 | sha1: 3E40C27D2A53C4E7878AA9DC5D638F99D3E4F544 | sha256: 09BB7D8D55FD373C124034A7AFDA3AA5E109E85C502EA3E3EBD03642CBC6869C | sha512: 0317A6BAD0ADE2660870F0F2ADCAD012CFB63CB99A4ED7818284A15B4A83E5C7A61886A820A64F59FDD78D1F5680868B9ED76C52F930436441D4E2A287F2681D
tools\LICENSE.txt
From: Program start dialog

"This program may be freely distributed in accordance with the license agreement."

===========================
From: Installation program window

LICENSE AGREEMENT

Chromas is copyright © 1998-2018 Technelysium Pty Ltd. All rights reserved.

IMPORTANT - READ CAREFULLY

This license statement constitutes a legal agreement ("License Agreement") 
between you ("Licensee", either as an individual or a single entity) and 
Technelysium Pty Ltd ("Licensor"), sole worldwide publisher of the software 
product Chromas ("Software") of which Technelysium Pty Ltd is the copyright holder.

The Web Site referred to in this agreement is http://www.technelysium.com.au

BY INSTALLING, COPYING, OR OTHERWISE USING THE SOFTWARE, YOU AGREE TO BE 
BOUND BY ALL OF THE TERMS AND CONDITIONS OF THE LICENSE AGREEMENT.

The Software is provided as-is.  No warranty or fitness for a particular 
purpose is expressed or implied.  In no event shall the Licensor or any 
of the Licensor's affiliates be liable for any consequential, special, 
incidental or indirect damages of any kind arising out of the delivery, 
performance or use of the Software, to the maximum extent permitted by law.  
The Software is not designed or intended to be used in any activity that 
may cause personal injury, death or any other severe damage or loss.

Upon your acceptance of the terms and conditions of the License Agreement, the 
Licensor grants you the right to use the Software in the manner provided below.

If you do not accept the terms and conditions of the License Agreement, you 
must promptly delete each and any copy of the Software from all your computers.

The Licensor reserves the right to license the same Software to other 
individuals or entities under a different license agreement.

After accepting this License Agreement, the Licensee is permitted to use 
the Software under the terms of this agreement, without payment to the 
Licensor, until such time as the Licensor withdraws the license to use 
the Software.

Technical support may be available directly from the Licensor.  When 
encountering problems, the Licensee must verify that the Licensee is using 
the latest version of the Software, by reading the product page on the Web 
Site. If the Licensee has the latest version, the Licensee may write to 
[email protected] with his or her question in the English language. 
The Licensor reserves the right to refuse to provide technical support.

You must not attempt to reverse compile, modify, translate or disassemble 
the Software in whole or in part.  You must not run the Software under a 
debugger or similar tool allowing you to inspect the inner workings of 
the Software.

The Software remains the exclusive property of the Licensor.

You must not ask payment for the act of distributing the installation 
package of the Software or for the Software itself.  You must not distribute 
the Software by making it part of a larger package, unless that package is 
a collection of free evaluation software and other software that does not 
require payment.

The Licensor reserves the right to revoke your license if you violate any 
or all of the terms of this license agreement, without prior notice.

****************************************************

Chromas includes a PeakTrace component provided by Nucleics Pty Ltd. The 
following license applies to the PeakTrace component:

END-USER LICENSE AGREEMENT ("EULA") FOR NUCLEICS PTY. LTD. PEAKTRACE 6 RP SOFTWARE

IMPORTANT-READ CAREFULLY: This Nucleics End-User License Agreement ("EULA") 
is a legal agreement between you (either an individual or a single entity) 
and Nucleics Pty. Ltd. ("Nucleics") for the PeakTrace RP software, which 
includes computer software and may include associated computer hardware, 
media, printed materials, and "online" or electronic documentation 
(collectively, "SOFTWARE"). By installing, copying, or otherwise using the 
SOFTWARE, you agree to be bound by the terms of this EULA. If you do not 
agree to the terms of this EULA, do not install, copy or otherwise use 
the SOFTWARE.

Software LICENSE

The SOFTWARE is protected by copyright laws and international copyright 
treaties, as well as other intellectual property laws and treaties. The 
SOFTWARE is licensed, not sold.

1. GRANT OF LICENSE

This EULA grants you the following limited, non-exclusive, nontransferable, 
non-assignable rights:

Installation and Use: You may ONLY use the SOFTWARE with .ab1, abd or abi 
file format data collected from DNA sequencing instruments. You may only 
use the SOFTWARE if you have a PeakTrace license.

Reserved Rights: Nucleics and its suppliers retain title and all ownership 
rights to the SOFTWARE. All rights not expressly granted are reserved to 
Nucleics.

2. DESCRIPTION OF OTHER RIGHTS AND LIMITATIONS

Limitations on Reverse Engineering, Decompilation, and Disassembly. You 
may not reverse engineer, decompile, or disassemble the SOFTWARE, except 
and only to the extent that such activity is expressly permitted by applicable 
law notwithstanding this limitation.

3. INTELLECTUAL PROPERTY RIGHTS

All title and intellectual property rights in and to the SOFTWARE 
(including but not limited to any images, photographs, animations, video, 
audio, music, text and "applets" incorporated into the SOFTWARE), and any 
copies you are permitted to make herein are owned by Nucleics or its 
suppliers. All title and intellectual property rights in and to the content 
which may be accessed through use of the SOFTWARE is the property of the 
respective content owner and may be protected by applicable copyright or 
other intellectual property laws and treaties. All rights not expressly 
granted are reserved by Nucleics.

4. CONTROLLING LAW AND SEVERABILITY

This EULA will be governed by and construed in accordance with the laws 
in the State of New South Wales, Australia, as applied to agreements 
entered into and to be performed entirely within New South Wales between 
New South Wales residents. This EULA shall not be governed by the United 
Nations Convention on Contracts for the International Sale of Goods, the 
application of which is expressly excluded. If for any reason a court of 
competent jurisdiction finds any provision, or portion thereof, to be 
unenforceable, the remainder of this EULA shall continue in full force 
and effect.

5. DISCLAIMER OF WARRANTIES

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF 
THE POSSIBILITY OF SUCH DAMAGE.

6. COMPLETE AGREEMENT; GOVERNING LANGUAGE

The warranty and remedies set forth above are exclusive and in lieu of 
all others, oral or written, express or implied. No Nucleics reseller, 
agent, or employee is authorized to make any modification, extension, or 
addition to this warranty. Any translation of this EULA is done for local 
requirements and in the event of a dispute between the English and any 
non-English versions, the English version of this EULA shall govern.

7. TERMINATION

This EULA is effective until terminated. Your rights under this EULA 
will terminate automatically without notice from Nucleics if you fail 
to comply with any term(s) of this EULA. Upon termination of this EULA, 
you shall cease all use of the SOFTWARE and destroy all copies, full or 
partial, of the SOFTWARE.

8. TRADEMARK AND LICENSES ACKNOWLEDGEMENTS

"PeakTrace", "PeakTrace RP", "Auto PeakTrace RP" and "Auto PeakTrace 6 RP" 
are trademarks of Nucleics Pty. Ltd.

The PeakTrace 6 RP installer provides the 7-Zip program. 7-Zip is 
licensed under the GNU LGPL license.You can receive a copy of the GNU 
Lesser General Public License from www.gnu.org. The source code for 
7-zip can be found at www.7-zip.org.

9. MISCELLANEOUS

Should you have any questions concerning this EULA, or if you desire to 
contact Nucleics for any reason, please write to: Nucleics Pty. Ltd, 
29 John St, Woollahra, NSW, 2025, Australia
tools\VERIFICATION.txt
VERIFICATION
Verification is intended to assist the Chocolatey moderators and community
in verifying that this package's contents are trustworthy.
 
The installer is available by following the download link on this page:  
   https://technelysium.com.au/wp/chromas/

Direct Download:

Version  : 2.6.6
URL      : http://www.technelysium.com.au/Chromas266Setup.exe
CheckSum : 09BB7D8D55FD373C124034A7AFDA3AA5E109E85C502EA3E3EBD03642CBC6869C


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
Chromas 2.6.5 85 Friday, October 12, 2018 Approved

This package has no dependencies.

Discussion for the Chromas Package

Ground Rules:

  • This discussion is only about Chromas and the Chromas 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.
  • The maintainers of this Chocolatey Package will be notified about new comments that are posted to this Disqus thread, however, it is NOT a guarantee that you will get a response. If you do not hear back from the maintainers after posting a message below, please follow up by using the link on the left side of this page or follow this link to contact maintainers. If you still hear nothing back, please follow the package triage process.
  • Tell us what you love about the package or Chromas, or tell us what needs improvement.
  • Share your experiences with the package, or extra configuration or gotchas that you've found.
  • If you use a url, the comment will be flagged for moderation until you've been whitelisted. Disqus moderated comments are approved on a weekly schedule if not sooner. It could take between 1-5 days for your comment to show up.
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