Mercurial > repos > yhoogstrate > package_unafold_3_8
changeset 0:9d157819abe5 draft default tip
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/unafold_galaxy_wrapper commit 9ac0b453ceb7370d9ae50bc2c26ae06c905c736b
| author | yhoogstrate |
|---|---|
| date | Tue, 16 Jun 2015 09:14:48 -0400 |
| parents | |
| children | |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 109 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Jun 16 09:14:48 2015 -0400 @@ -0,0 +1,109 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="unafold" version="3.8"> + <install version="1.0"> + <actions> + <action type="shell_command"> + wget http://homepages.rpi.edu/~zukerm/download/unafold-3.8.tar.gz && + tar -zxvf unafold-3.8.tar.gz && + cd unafold-3.8 && + ./configure --prefix=$INSTALL_DIR && + make && + make install + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <!--<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>--> + </action> + </actions> + </install> + <readme> + Downloads and installs UNAFold. + + Prerequisites: + - perl + - wget + - tar + - gnu-autotools (make) + + + License + ------- + + UNAFold 3.x ACADEMIC NON-COMMERCIAL USE LICENSE AGREEMENT + +1. UNAFold 3.x is the work of Drs. Nicholas R. Markham and Michael Zuker. The + copyright in UNAFold 3.x is owned by RENSSELAER POLYTECHNIC INSTITUTE. + +2. This is a legal agreement between you, RECIPIENT, and RENSSELAER POLYTECHNIC + INSTITUTE. By accepting, receiving, and using UNAFold 3.x, you agree to be + bound by all of its terms. If you do not agree to all of the terms of this + Agreement, please DO NOT download the software; or, if you have already done + so, please delete all of the source code, documentation and compiled programs + associated with UNAFold 3.x. + +3. UNAFold 3.x is provided to RECIPIENT as source code. RENSSELAER POLYTECHNIC + INSTITUTE grants to RECIPIENT a royalty free, non-exclusive, and non- + transferable license to compile, install, use UNAFold for internal research + only. RECIPIENT acknowledges that UNAFold 3.x is a research tool that is + provided free of charge and only provided "as is." RENSSELAER POLYTECHNIC + INSTITUTE, its faculty, employees, or students, or former employees who have + developed UNAFold 3.x, have no obligation to assist RECIPIENT in its use, + correction, modification, or enhancement and are without any obligation to + provide any updates. RECIPIENT may also offer UNAFold 3.x to the public over + a web server provided the program resides on a server at RECIPIENT's + institution and users are not able to download or modify the program. + +4. The title and copyright to UNAFold 3.x and any associated programs and + documentation shall remain with RENSSELAER POLYTECHNIC INSTITUTE. RECIPIENT + agrees to preserve same. RECIPIENT agrees not to make any copies of UNAFold + except for use in RECIPIENT's laboratory without RENSSELAER POLYTECHNIC + INSTITUTE's prior written permission. Written permission can be obtained by + contacting Rensselaer Polytechnic Institute's Office of Technology + Commercialization by e-mail at burtok2@rpi.edu, or by telephone at 518-276- + 3675. RECIPIENT agrees to place the appropriate copyright notice on any such + copies. + +5. RECIPIENT may not modify UNAFold 3.x, except to fix minor errors, or create + derivative works without RENSSELAER POLYTECHNIC INSTITUTE's permission. + Please send all requests for modification to markhn@rpi.edu and + zukerm@rpi.edu. Errors and bugs that are found should be reported to Nick + Markham and Michael Zuker, whether or not they are corrected. + +6. RECIPIENT shall not distribute UNAFold 3.x to other laboratories within + RECIPIENT's institution. RECIPIENT shall not transfer UNAFold 3.x to another + location or person outside of RECIPIENT's institution without RENSSELAER + POLYTECHNIC INSTITUTE's prior written permission. Please send all requests + for distribution to markhn@rpi.edu and zukerm@rpi.edu. + +7. If RENSSELAER POLYTECHNIC INSTITUTE grants RECIPIENT permission to distribute + UNAFold 3.x, under Paragraph 6, RECIPIENT shall only export UNAFold 3.x or + any part thereof, directly or indirectly, to any country where such export or + reexport is authorized in full compliance with the laws of the United States + of America. + +8. RECIPENT shall cite the following publications in any abstract, paper, or + presentation referencing UNAFold: + +a. N. Markham & M. Zuker. (2003) DINAMelt web server for nucleic acid melting + prediction. Nucleic Acids Res. 33:W577-W581. + +9. RECIPIENT acknowledges that as UNAFold 3.x is a research tool and provided + free of charge, it is only provided "as is." RENSSELAER POLYTECHNIC + INSTITUTE, its faculty, employees, or students, have no obligation to assist + RECIPIENT in its use, correction, modification, or enhancement and are + without any obligation to provide any updates. + +10. RENSSELAER POLYTECHNIC INSTITUTE MAKES NO REPRESENTATIONS AND EXTENDS NO + WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED. THERE ARE NO EXPRESS OR + IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS OF UNAFold 3.x FOR A + PARTICULAR PURPOSE, OR THAT THE USE OF UNAFold 3.x WILL NOT INFRINGE ANY + PATENT, COPYRIGHT, TRADEMARK, TRADE SECRET, OR OTHER INTELLECTUAL PROPERTY + RIGHTS OF ANOTHER PARTY, OR ANY OTHER EXPRESS OR IMPLIED WARRANTIES. + RENSSELAER POLYTECHNIC INSTITUTE WILL NOT BE LIABLE TO RECIPIENT FOR ANY + CLAIMS OR DAMAGES ARISING FROM YOUR RECIPIENT'S OF UNAFold 3.x, ANY CLAIM + FOR ANY LOSS OR INTERRUPTION OF BUSINESS, OR FOR ANY INDIRECT, SPECIAL, OR + CONSEQUENTIAL DAMAGES OF ANY KIND. + </readme> + </package> +</tool_dependency>