Skip to content

Commit

Permalink
Set AGPL license
Browse files Browse the repository at this point in the history
  • Loading branch information
@jordeu
jordeu committed May 20, 2016
1 parent 72eefcf commit 559cf5b
Show file tree
Hide file tree
Showing 2 changed files with 16 additions and 190 deletions.
196 changes: 13 additions & 183 deletions LICENSE
View file
Original file line number Diff line number Diff line change
@@ -1,32 +1,18 @@
UPF FREE SOURCE CODE LICENSE AGREEMENT
UNIVERSITAT POMPEU FABRA
Free Source Code License Agreement
OncodriveFML is the property of the Universitat Pompeu Fabra (UPF), which hold the copyright thereto.
Copyright (C) 2016 Universitat Pompeu Fabra

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as
published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.

UNIVERSITAT POMPEU FABRA (“UPF”) LICENSES THE SOFTWARE IDENTIFIED BELOW TO YOU ONLY UPON THE CONDITION THAT
YOU ACCEPT ALL OF THE TERMS CONTAINED IN THIS FREE BINARY CODE LICENSE AGREEMENT (“LICENSE”). PLEASE READ
THE LICENSE TERMS CAREFULLY. BY DOWNLOADING OR INSTALLING THIS SOFTWARE, OR INDICATING ACCEPTANCE BY SELECTING
THE "ACCEPT" BUTTON ON ANY DOWNLOAD OR INSTALL FUNCTION, YOU ACCEPT THE TERMS OF THE LICENSE.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.


SUMMARY TABLE
Key Terms
Software:
OncodriveFML
Licensor
Universitat Pompeu Fabra, with registered address at Plaça de la Mercè, 10-12, 08002 Barcelona, Spain
Licensee
NAME
ADDRESS
IDENTIFICATION
Permitted purposes:
Academic, non-commercial, and personal use only permitted
Duration
1 year


IN WITNESS WHEREOF, the parties agree to the terms and conditions of this Agreement. The signatories warrant
they are duly authorised by their organisations to enter into this agreement on behalf of such organisation.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>


Notices/Contact
Expand All @@ -39,160 +25,4 @@ Notices/Contact
Att.:

Telephone: +34 93 542 15 67
Email: [email protected]

________________

Terms and Conditions


1. DEFINITIONS.
"Software" means the software programs identified herein in binary or source code form, any other machine
readable materials (including, but not limited to, libraries, source files, header files, and data files),
any updates or error corrections provided by UPF, and any user manuals, APIs, programming guides and other
documentation provided to you by UPF under this Agreement.

"Source Code" shall include computer programming code or any computer instructions necessary to compile the Software.

"Derivative Works" means any software programs which are developed by Licensee and which incorporate or
contain modifications of any part of Source Code, and including any revision, modification, translation
(including compilation or recapitulation by computer), abridgment, condensation, expansion or any other
form in which Source Code, may be recast, transformed or adapted.

"Purpose" means, unless otherwise specified in the Summary Table, the creation of enhancements, revisions,
modifications and adaptations of Source Code, and addition of new user interfaces, features and functionality
to the Software, and bug-fixes and corrections to the above.


2. LICENSE. Subject to the terms and conditions of this License, UPF grants you a royalty-free, worldwide,
non-exclusive, non-transferable, non-sublicensable, limited license for the specified duration, to
(a) use and reproduce as many copies of the Source Code as are reasonably necessary only for the purpose
of exercising the rights granted under this Agreement; and
(b) modify the Software and create Derivative Works, and use and reproduce them for the Purpose.


3. CONDITIONS. The Software is confidential and copyrighted. Unless enforcement is prohibited by applicable
law and other than as expressly provided in the Summary Table above, you may not:
(a) use and/or copy the Software in whole or in part for any purpose other than as indicated;
(b) disclose, distribute, sell, lease, license or communicate the Software in any way or otherwise make it available
to third parties, including uploading to Internet;
(c) cause or permit anyone to modify, decompile, disassemble, decrypt, extract or otherwise or reverse engineer
the Software; or
(d) export, directly or indirectly, the Software in violation of any applicable export control laws in any jurisdiction.

The terms of this Agreement do not entitle you to receive any support or maintenance services from UPF with
respect to the Software. You may make one backup copy. In the event Software contains source code, unless
expressly licensed for other purposes, it is provided solely for reference purposes pursuant to the terms of
this License. Source code may not be redistributed unless expressly provided for in this License.


4. INTELLECTUAL AND INDUSTRIAL PROPERTY RIGHTS. Title to Software and all associated intellectual and industrial
property rights is retained by UPF and/or its licensors. UPF warrants that the copyright in the Software is owned
by it or licensed to it and that it has the power and authority to grant the Licence. You shall keep intact all
authorship, copyright, patent or trademark notices and all notices that refer to the Software and the Licence
and to the disclaimer of warranties.


5. CONFIDENTIALITY AND PROPRIETARY. You agree and acknowledge that the Source Code is proprietary, valuable,
and not generally known in the industry. You agree that you will maintain, through reasonable means, the
confidentiality of the Source Code, and will not disseminate or allow unrestricted access. You shall not distribute
the Source Code to anyone other than employees and software developers of your organization or third party contractors
working on behalf of your organization with a need to know and subject to confidentiality obligations.
You may be held legally responsible for any infringement of intellectual property rights that is caused or
encouraged by your failure to abide by this Agreement.


7. DISCLAIMER OF WARRANTY. This Software is a work in progress. It is not a finished work and may therefore
contain defects or “bugs” inherent to this type of software development. For this reason, to the maximum extent
permitted by obligatorily applicable law, the Software is provided on an “as is” basis and without warranties
of any kind, including without limitation satisfactory quality and conformity, merchantability, fitness for a
particular purpose, absence of defects or errors, accuracy, or non-infringement of intellectual or industrial
property rights other than copyright as stated in Article 4 of this Licence. This disclaimer of warranty is
an essential part of the Licence and a condition for the grant of any rights to the Software.

8. LIMITATION OF LIABILITY. Except in the cases of wilful misconduct or physical damages directly caused to
natural persons, and to the maximum extent permitted by obligatorily applicable law, in no event will UPF or
its licensors be liable for any direct or for indirect or consequential damages, however caused, arising out
of or related to the use of or inability to use Software; including without limitation, damages for loss of
goodwill, work stoppage, computer failure or malfunction, loss of data or any commercial damage and lost
revenue or profit, even if the UPF has been advised of the possibility of such damage. However, the UPF will
be liable under statutory product liability laws as far such laws apply to the UPF and to the Software. The
foregoing limitations will apply even if the above stated warranty disclaimer fails of its essential purpose.
Some jurisdictions do not allow the exclusion of indirect or consequential damages, so some of the terms above
may not be applicable to you.


9. AUDIT. Upon 5 days written notice, UPF or a professional designated by UPF may audit your use of the Software.
You agree to cooperate with UPF’s audit and provide reasonable assistance and access to information. You agree
to pay within 30 days of written notification any fees applicable to your use of the Software in breach of your
license rights. If you do not pay, UPF can end your license. You agree that UPF shall not be responsible for any
of your costs incurred in cooperating with the audit.


10. TERMINATION. This Agreement is effective until terminated. You may terminate this Agreement at any time by
destroying all copies of Software. This Agreement will terminate immediately without notice from UPF if you fail
to comply with any provision of this Agreement. Either party may terminate this Agreement immediately should
any Software become, or in either party's opinion be likely to become, the subject of a claim of infringement
of any intellectual or industrial property right. Upon Termination, you must destroy all copies of Software.
Provisions that survive termination or expiration include those relating to limitation of liability limitation
and others which by their nature are intended to survive, and apply to both parties' respective successors
and assignees.


11. EXPORT REGULATIONS. Software and technical data delivered under this Agreement may be subject to export or
import regulations. You agree to comply strictly with all such laws and regulations and acknowledge that you
have the responsibility to obtain such licenses to export, re-export, or import as may be required after
delivery to you.


12. TRADEMARKS. This Licence does not grant permission to use the trade names, trademarks, service marks,
or names of the UPF, except as required for reasonable and customary use in describing the origin of the
Software and reproducing the content of the copyright notice.


13. GOVERNING LAW / JURISDICTION. Any action related to this Agreement will be governed by Spanish law.
No choice of law rules of any jurisdiction will apply. Any action, conflict or dispute resulting from
this License and use of the Software will be subject to the exclusive jurisdiction of the courts of the
City of Barcelona, Spain.


14. SEVERABILITY If any provision of the Licence is invalid or unenforceable under applicable law, this
will not affect the validity or enforceability of the Licence as a whole. Such provision will be construed
and/or reformed so as necessary to make it valid and enforceable. If this is not possible, the License
will terminate.


15. ASSIGNMENT. You may not assign this agreement or give or transfer the Software or an interest in it
to another individual or entity. If you grant a security interest in the Software, the secured party has
no right to use or transfer the Software.


16. FORCE MAJEURE: Neither party shall be responsible for failure to fulfil any obligation due to causes
beyond its control. This section does not excuse either party's obligation to take reasonable steps to
follow its normal disaster recovery procedures.


17. NO THIRD PARTY RIGHTS. No right or cause of action for any third party is created by this Agreement,
nor is UPF responsible for any third party claims against Licensee.


18. DATA PROTECTION: Licensee authorises UPF to process and use the contact information set out above in
support of Licensee and for the purpose of managing and furthering the relationship between UPF and Licensee
including, without limitation, contacting such persons by email. Such information will be processed in
accordance with Spanish Data Protection law. Licensee represents that it has obtained the required consent
from contact personnel as are necessary for this purpose.


19. INTEGRITY. This Agreement is the entire agreement between you and UPF relating to its subject matter.
It supersedes all prior or contemporaneous oral or written communications, proposals, representations and
warranties and prevails over any conflicting or additional terms of any quote, order, acknowledgment, or
other communication between the parties relating to its subject matter during the term of this Agreement.
No modification of this Agreement will be binding, unless in writing and signed by an authorised representative
of each party.


NOTICE: Third Party Code. Additional copyright notices and license terms applicable to portions of the
Software are set forth in the LICENSING.txt. file.


For inquiries please contact: UPF at the address indicated for notices.
Email: [email protected]
10 changes: 3 additions & 7 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -62,12 +62,6 @@ The following command will show you the command help:
multiply to the signature probability
--no-figures Output only the tsv results file

Indels options:
-D INDELS_FILE, --indels INDELS_FILE
Indels scores file
--indels-background INDELS_BACKGROUND
Indels random background scores

Execution options:
--cores CORES Maximum CPU cores to use (default all available)
--debug Show more progress details
Expand All @@ -85,7 +79,7 @@ The following command will show you the command help:
## File formats ##

**TIP**: All the files can be compressed using GZIP (extension ".gz"), BZIP2 (ext. ".bz2") or LZMA (ext. ".xz")
> **TIP**: All the files can be compressed using GZIP (extension ".gz"), BZIP2 (ext. ".bz2") or LZMA (ext. ".xz")
### Input file format ###

Expand Down Expand Up @@ -120,6 +114,8 @@ if you first download it using our data package managment tool that is also inst
Run this command to download the CADD scores file to the default bgdata folder `~/.bgdata`:

$ bg-data -n 10 genomicscores cadd 1.3

> **WARNING**: CADD scores are original from http://cadd.gs.washington.edu/ and are freely available for all non-commercial applications. If you are planning on using them in a commercial application, please contact them at http://cadd.gs.washington.edu/contact.
Also if you want to speed up the download of the genome reference that is also needed, run this command:

Expand Down

0 comments on commit 559cf5b

Please sign in to comment.