From 2f6caac6019e3182486965f7f09baed7e93e1be9 Mon Sep 17 00:00:00 2001 From: "A. Wilcox" Date: Sun, 11 Jun 2017 08:41:26 +0000 Subject: The New Plan ebuild branch has old ebuilds. profiles dir still has CFLAGS. Everything else is removed or modified for changing of upstream to Alpine. --- licenses/phrap | 210 --------------------------------------------------------- 1 file changed, 210 deletions(-) delete mode 100644 licenses/phrap (limited to 'licenses/phrap') diff --git a/licenses/phrap b/licenses/phrap deleted file mode 100644 index 0e1df110a..000000000 --- a/licenses/phrap +++ /dev/null @@ -1,210 +0,0 @@ -ACADEMIC USER AGREEMENT - -Please read the entire agreement, fill in the information in the -indicated positions (such as "NAME:"), and return the entire document -to the indicated people. Please send the document as the message--not -as an attachment. - -Phrap: A program for assembling DNA sequence data. - -Swat: A program for searching one or more DNA or protein query sequences -against a sequence database, using (an efficient implementation of) the -Smith-Waterman-Gotoh algorithm. - -Cross_Match: A general-purpose utility based on Swat for comparing any -two sets of (long or short) DNA sequences. - -Phred: A program that reads DNA sequencer trace data, calls bases, -assigns quality values to the bases, and writes the base calls and quality -values to output files. - -Consed: A program for viewing and editing Phrap assemblies. - -To receive any of these programs you will need to agree to the following -conditions. They should be taken seriously! - -1) You agree to read the documentation. We welcome feedback on any -inaccuracies. - -2) You agree to report any bugs to us. (To fix bugs, we will need -from you a dataset and a procedure that reproduces the problem; but do -not send datasets without first emailing us to describe the nature of -the bug.) - -3) You agree not to make the programs (including source code, -executables, or any part thereof, in modified or unmodified form) -available to anyone outside your group, and not to put them where they -may be accessible to outside individuals without your direct knowledge -(e.g. on a computer to which people outside your group have login -privileges). The documentation however may be freely distributed. -Refer any requests for the programs to the authors. If you are -operating a computer facility which provides access to several -independent investigators, you agree to set the permissions on the -executables and source code to allow execute but not read access, so -that the programs may not be copied. Investigators who want copies of -the software for their own use must return a separate copy of this -agreement. - -4) You agree not to use the programs for any commercial purpose, -including but not limited to commercially restricted sequencing -(defined as sequencing for which a company retains patenting or -licensing rights regarding the sequence, or the right to restrict or -delay dissemination of the sequence; with the sole exception that -sequencing is not considered to be commercially restricted if it is -federally funded and the investigators adopt the data release policies -endorsed at the Wellcome Trust-sponsored Bermuda meeting, -i.e. immediate release of data as it is generated). - [If you wish to obtain the software for commercially restricted -sequencing or any other commercial purposes, you will need to execute -a separate licensing agreement with the University of Washington and -pay a fee. In that case please contact: - -Lisa Heinz -University of Washington TechTransfer, Digital Ventures -Box 354990 -4311-11th Avenue NE, Suite 500 -Seattle, WA 98105-4608 - -http://depts.washington.edu/techtran - -206-616-3451 FAX: 206-616-3322 -swxfr@u.washington.edu - -Do not contact her if the academic license applies.] - -5) You acknowledge that the software is experimental in nature and is -supplied "AS IS", without obligation by the authors or the University -of Washington to provide accompanying services or support. The entire -risk as to the quality and performance of the Software is with you. -UW AND THE AUTHORS EXPRESSLY DISCLAIM ANY AND ALL WARRANTIES -REGARDING THE SOFTWARE, WHETHER EXPRESS OR IMPLIED, INCLUDING BUT NOT -LIMITED TO WARRANTIES PERTAINING TO MERCHANTABILITY OR FITNESS FOR A -PARTICULAR PURPOSE. - -6) All members of your group with access to the software agree to the -same conditions. - - - -Having read the above, if you are still interested in obtaining the -programs, please return a copy of this entire message (which MUST be -included so that it is clear what you are agreeing to) by email -together with the following information: - -NAME: Your name in first name/last name order. - -NAME: - - -Example: -NAME: John Dracula -(Please do not use all capitals such as John DRACULA) - -ACKNOWLEDGEMENT: An acknowledgement that you and the members of your -group agree to these conditions. - -ACKNOWLEDGEMENT: - -Example: -ACKNOWLEDGEMENT: I agree to the license. - -PROGRAMS: Which programs you want (phrap,cross_match, and swat are -distributed together). You must cc the message to each appropriate -individual (Brent Ewing, David Gordon, and/or Phil Green) at the email -addresses below so that they will know to send you the appropriate -program. - -PROGRAMS: - -Example: -PROGRAMS: phred, phrap, consed - -INSTITUTION: Your academic or government institution (give full name, -not abbreviation) - -INSTITUTION: - -Example: -INSTITUTION: University of Lower Transylvania - -DEPARTMENT: Your department - -DEPARTMENT: - -Example: -DEPARTMENT: Department of Hematology - -EMAIL: Your email address for all future correspondence. Ideally this -should be a Unix computer running a generic mail program, since -several of the programs are sent as uuencoded files which may be -corrupted by some mail programs. - If this address is not at the institution & department listed above, -please explain the discrepancy. - -EMAIL: - -Example: -EMAIL: john.dracula@utrans.edu - -OS: (Consed requestors only) Which platform(s) you want Consed for: -solaris 2.5.1, solaris 2.6, solaris 2.7 (solaris 7), solaris 8, -solaris 9, digital unix 4.0 (or better), hp-ux 11.x, sgi irix 6.2, -6.3, 6.4, or 6.5, linux (normal 32 bit) (Redhat 7.1-1 or better), -linux (Itanium), linux (AMD64), ibm aix 5.2 (or better), macosx 10.2 -(Darwin kernel 6.0) (or better), or solaris-intel (2.8 or better). - -OS: - -Example: -OS: hpux - -Note: Consed is not available for PC's running Windows, XP, NT, or -2000. - -IP: (Consed requestors only) The ip address of the computer on which -you will be running a web browser to download consed. This does not -have to be the same computer as the one on which you will run consed. -Please view page -http://bozeman.mbt.washington.edu/consed/find_ip_address.html -which will tell you what my computer thinks is your ip address. - -(Even if you think you know your ip address, firewalls and proxies can -cause your browser to transmit a different ip address, and thus my -webserver would deny you access to consed. So it would be a good idea -to view the page above and send me the ip address it shows, even if -this isn't your real ip address.) - -IP: - -Example: -IP: 123.49.74.80 - - -If you want Consed/Autofinish, you must include OS and IP (above). -Consed cannot be obtained without them. - -Please return this entire agreement so it is clear what you are -agreeing to. - -Please send all of this, including the agreement, as part of the -email message--not as an attachment. - -Send it to each of the relevant individuals below: - -Contacts for obtaining the programs and for questions, bug reports, -suggestions: - - Phrap/cross_match/swat: Phil Green, phg (at) u.washington.edu - Phred: Brent Ewing, bge (at) u.washington.edu - Consed: David Gordon, gordon (at) genome.washington.edu - -where the " (at) " is replaced by "@". - -It can take up to 2 weeks for a license application to be processed, -so please be patient. - - - - - - -- cgit v1.2.3-60-g2f50