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Chromas

2.6.6

Package test results are passing.

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

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.

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

C:\> choco install chromas

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

C:\> choco upgrade chromas

Files

Hide
  • tools\chocolateyinstall.ps1 Show
    $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 Show
    md5: 3C4663B431305421BE750C4F6AF3A993 | sha1: 3E40C27D2A53C4E7878AA9DC5D638F99D3E4F544 | sha256: 09BB7D8D55FD373C124034A7AFDA3AA5E109E85C502EA3E3EBD03642CBC6869C | sha512: 0317A6BAD0ADE2660870F0F2ADCAD012CFB63CB99A4ED7818284A15B4A83E5C7A61886A820A64F59FDD78D1F5680868B9ED76C52F930436441D4E2A287F2681D
  • tools\LICENSE.txt Show
    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 Show
    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
    
    

Virus Scan Results

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.

Dependencies

This package has no dependencies.

Package Maintainer(s)

Software Author(s)

  • Technelysium

Copyright

copyright © 1998-2018 Technelysium Pty Ltd.

Tags

Release Notes

https://technelysium.com.au/wp/chromas-version-history/

Version History

Version Downloads Last updated Status
Chromas 2.6.5 59 Friday, October 12, 2018 approved

Discussion for the Chromas Package

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  • 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.
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  • 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.
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