From 56bd759df1d0c750a065b8c845e93d5dfa6b549d Mon Sep 17 00:00:00 2001 From: "Robin H. Johnson" Date: Sat, 8 Aug 2015 13:49:04 -0700 Subject: proj/gentoo: Initial commit MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson X-Thanks: Alec Warner - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring - wrote much python to improve cvs2svn X-Thanks: Rich Freeman - validation scripts X-Thanks: Patrick Lauer - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed --- licenses/phrap | 210 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 210 insertions(+) create mode 100644 licenses/phrap (limited to 'licenses/phrap') diff --git a/licenses/phrap b/licenses/phrap new file mode 100644 index 000000000000..0e1df110ade2 --- /dev/null +++ b/licenses/phrap @@ -0,0 +1,210 @@ +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 v1.2.3-65-gdbad