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weaver 08/12/31 00:20:14 |
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Added: phrap |
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Log: |
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New license phrap for sci-biology/phrap |
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Revision Changes Path |
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1.1 licenses/phrap |
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file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/licenses/phrap?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/licenses/phrap?rev=1.1&content-type=text/plain |
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Index: phrap |
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=================================================================== |
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ACADEMIC USER AGREEMENT |
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|
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Please read the entire agreement, fill in the information in the |
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indicated positions (such as "NAME:"), and return the entire document |
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to the indicated people. Please send the document as the message--not |
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as an attachment. |
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|
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Phrap: A program for assembling DNA sequence data. |
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|
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Swat: A program for searching one or more DNA or protein query sequences |
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against a sequence database, using (an efficient implementation of) the |
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Smith-Waterman-Gotoh algorithm. |
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|
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Cross_Match: A general-purpose utility based on Swat for comparing any |
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two sets of (long or short) DNA sequences. |
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|
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Phred: A program that reads DNA sequencer trace data, calls bases, |
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assigns quality values to the bases, and writes the base calls and quality |
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values to output files. |
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|
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Consed: A program for viewing and editing Phrap assemblies. |
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|
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To receive any of these programs you will need to agree to the following |
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conditions. They should be taken seriously! |
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|
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1) You agree to read the documentation. We welcome feedback on any |
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inaccuracies. |
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|
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2) You agree to report any bugs to us. (To fix bugs, we will need |
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from you a dataset and a procedure that reproduces the problem; but do |
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not send datasets without first emailing us to describe the nature of |
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the bug.) |
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|
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3) You agree not to make the programs (including source code, |
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executables, or any part thereof, in modified or unmodified form) |
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available to anyone outside your group, and not to put them where they |
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may be accessible to outside individuals without your direct knowledge |
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(e.g. on a computer to which people outside your group have login |
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privileges). The documentation however may be freely distributed. |
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Refer any requests for the programs to the authors. If you are |
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operating a computer facility which provides access to several |
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independent investigators, you agree to set the permissions on the |
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executables and source code to allow execute but not read access, so |
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that the programs may not be copied. Investigators who want copies of |
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the software for their own use must return a separate copy of this |
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agreement. |
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|
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4) You agree not to use the programs for any commercial purpose, |
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including but not limited to commercially restricted sequencing |
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(defined as sequencing for which a company retains patenting or |
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licensing rights regarding the sequence, or the right to restrict or |
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delay dissemination of the sequence; with the sole exception that |
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sequencing is not considered to be commercially restricted if it is |
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federally funded and the investigators adopt the data release policies |
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endorsed at the Wellcome Trust-sponsored Bermuda meeting, |
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i.e. immediate release of data as it is generated). |
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[If you wish to obtain the software for commercially restricted |
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sequencing or any other commercial purposes, you will need to execute |
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a separate licensing agreement with the University of Washington and |
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pay a fee. In that case please contact: |
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|
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Lisa Heinz |
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University of Washington TechTransfer, Digital Ventures |
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Box 354990 |
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4311-11th Avenue NE, Suite 500 |
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Seattle, WA 98105-4608 |
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|
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http://depts.washington.edu/techtran |
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|
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206-616-3451 FAX: 206-616-3322 |
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swxfr@××××××××××××.edu |
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Do not contact her if the academic license applies.] |
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5) You acknowledge that the software is experimental in nature and is |
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supplied "AS IS", without obligation by the authors or the University |
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of Washington to provide accompanying services or support. The entire |
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risk as to the quality and performance of the Software is with you. |
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UW AND THE AUTHORS EXPRESSLY DISCLAIM ANY AND ALL WARRANTIES |
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REGARDING THE SOFTWARE, WHETHER EXPRESS OR IMPLIED, INCLUDING BUT NOT |
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LIMITED TO WARRANTIES PERTAINING TO MERCHANTABILITY OR FITNESS FOR A |
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PARTICULAR PURPOSE. |
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6) All members of your group with access to the software agree to the |
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same conditions. |
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Having read the above, if you are still interested in obtaining the |
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programs, please return a copy of this entire message (which MUST be |
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included so that it is clear what you are agreeing to) by email |
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together with the following information: |
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NAME: Your name in first name/last name order. |
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NAME: |
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Example: |
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NAME: John Dracula |
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(Please do not use all capitals such as John DRACULA) |
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ACKNOWLEDGEMENT: An acknowledgement that you and the members of your |
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group agree to these conditions. |
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ACKNOWLEDGEMENT: |
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|
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Example: |
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ACKNOWLEDGEMENT: I agree to the license. |
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PROGRAMS: Which programs you want (phrap,cross_match, and swat are |
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distributed together). You must cc the message to each appropriate |
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individual (Brent Ewing, David Gordon, and/or Phil Green) at the email |
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addresses below so that they will know to send you the appropriate |
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program. |
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PROGRAMS: |
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Example: |
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PROGRAMS: phred, phrap, consed |
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INSTITUTION: Your academic or government institution (give full name, |
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not abbreviation) |
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INSTITUTION: |
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Example: |
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INSTITUTION: University of Lower Transylvania |
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DEPARTMENT: Your department |
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DEPARTMENT: |
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Example: |
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DEPARTMENT: Department of Hematology |
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EMAIL: Your email address for all future correspondence. Ideally this |
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should be a Unix computer running a generic mail program, since |
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several of the programs are sent as uuencoded files which may be |
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corrupted by some mail programs. |
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If this address is not at the institution & department listed above, |
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please explain the discrepancy. |
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EMAIL: |
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Example: |
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EMAIL: john.dracula@××××××.edu |
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|
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OS: (Consed requestors only) Which platform(s) you want Consed for: |
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solaris 2.5.1, solaris 2.6, solaris 2.7 (solaris 7), solaris 8, |
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solaris 9, digital unix 4.0 (or better), hp-ux 11.x, sgi irix 6.2, |
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6.3, 6.4, or 6.5, linux (normal 32 bit) (Redhat 7.1-1 or better), |
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linux (Itanium), linux (AMD64), ibm aix 5.2 (or better), macosx 10.2 |
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(Darwin kernel 6.0) (or better), or solaris-intel (2.8 or better). |
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OS: |
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Example: |
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OS: hpux |
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Note: Consed is not available for PC's running Windows, XP, NT, or |
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2000. |
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IP: (Consed requestors only) The ip address of the computer on which |
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you will be running a web browser to download consed. This does not |
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have to be the same computer as the one on which you will run consed. |
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Please view page |
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http://bozeman.mbt.washington.edu/consed/find_ip_address.html |
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which will tell you what my computer thinks is your ip address. |
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(Even if you think you know your ip address, firewalls and proxies can |
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cause your browser to transmit a different ip address, and thus my |
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webserver would deny you access to consed. So it would be a good idea |
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to view the page above and send me the ip address it shows, even if |
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this isn't your real ip address.) |
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IP: |
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Example: |
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IP: 123.49.74.80 |
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If you want Consed/Autofinish, you must include OS and IP (above). |
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Consed cannot be obtained without them. |
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Please return this entire agreement so it is clear what you are |
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agreeing to. |
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Please send all of this, including the agreement, as part of the |
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email message--not as an attachment. |
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Send it to each of the relevant individuals below: |
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Contacts for obtaining the programs and for questions, bug reports, |
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suggestions: |
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Phrap/cross_match/swat: Phil Green, phg (at) u.washington.edu |
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Phred: Brent Ewing, bge (at) u.washington.edu |
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Consed: David Gordon, gordon (at) genome.washington.edu |
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where the " (at) " is replaced by "@". |
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It can take up to 2 weeks for a license application to be processed, |
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so please be patient. |